You need to have successfully installed Squawkbox + the Tips and Procedures in Step 2 before proceeding.

For clarification purposes only.

Suppose we are AFA1900 sitting at gate B19 in Atlanta (KATL) and planning on flying to Charlotte (KCLT).

Our route is: KATL EATWO GRD UNARM1 KCLT (to find a route see #5, for charts see #6 of step 2) and our cruising altitude is FL230.

In the US Flight levels start at 18000ft. Below FL290 there is 1000ft of vertical seperation, to figure out which FL to use you need to use the SWEVEN, NEODD rule. This rule says that when you fly South or West you need to have an EVEN FL (eg. FL220) and when you fly North or East an ODD FL (eg. FL230). Above FL290 there is 2000ft seperation and thus 4000 ft of vertical seperation between same bound flights. In other words FL290, FL330, FL370, FL410 etc are valid flightlevels for eastbound flights. While FL310, FL350, FL390, FL430 etc are valid westbound flights. Other rules may apply in Europe and other parts of the world and thereīs a wealth of information on each of their sites.

How to read a route
The route in our example looks like this KATL ATL5.EATWO GRD.UNARM1 KCLT.

KATL is the ICAO code for Atlanta, GA your departure airport while KCLT stands for Charlotte, NC our destination. Click on the links to view the chart (opens in a new window).
ATL5.EATWO : ATL5 is the name of the DP formerly also known as SID which respectively stand for Departure Procedure and Standard instrument departure. EATWO (pronounced as East 2) is the transition on the Atlanta 5 departure.
GRD.Unarm1 : Unarm1 is the STANDARD TERMINAL ARRIVAL (STAR) for KCLT and GRD is the first waypoint on our route for this arrival.
Both DPīs and STARīs are used to organise traffic in such a way to minimize delays. If everyone were to fly his own route the skies above us would be a mess and collisions would be inevitable.

Again you can download charts for free as you need them from Myairplane.com . I suggest you certainly print out the charts of airports you will frequently visit. Put all the charts you print in a binder for future use. Since we are flying on FS you can use 'obsolete' charts. So no need to reprint every month or even year the charts.

Since this is not a tutorial on how to fly IFR, I will only quickly deal with how to fly these STARs etc. We have some great training manuals in the APG training Department and I suggest you take a look at it.

Lets fly!
You got the charts printed out or have them open in a webbrowser, your plane is fueled, doors are closed, passengers are seated, itīs time to depart.

Who to contact? You should have read this in Step 2 already but lets go over it together one more time.
Atlanta delivery, atlanta ground, nor atlanta approach or departure are online in this example, but Atlanta Tower and Atlanta Center are. Since Atlanta tower is the 'lowest' in rank we will contact him for our clearance (again right click in SB, then ATC directory and selecy ATL_V_TWR 119.5)

You are now with ATL_V_TWR on 119.5 (notice that the comm1 in your plane is automatically set to 119.5 and that if you selected 'use RW' upon connecting that you are also in his voice room now.)

Text in Green denotes that the pilot is speaking.
Text in Blue denotes the controller is speaking.

AFA1900: Atlanta tower, AFA1900 is requesting IFR clearance as filed. (Notice that when requesting something you first say the callsign of the person talking to and than your callsign)
ATL_V_TWR: AFA1900, clearance is on request standby
AFA1900: Standing by, AFA1900 ( when reading back an instruction, state your callsign at the end.)
... a little bit later ...
ATL_V_TWR: AFA1900, are you ready to copy your clearance?
AFA1900: Ready to copy, AFA1900 (Have a sheet of paper ready to write down the clearance, you will need to read it back.)
ATL_V_TWR: AFA1900, you are cleared to KCLT as filed, radar vectors on the Atl 5 dep, eatwo transition, climb and maintain (c/m) 10k, expect FL230 10min after departure, departure frequency 133.9, squawk (sq) 5401 (you can use abbreviations to readback)
AFA1900: Clrd to KCLT a/f, c/m 10k, expect FL230 in 10, dep freq 133.9, sq 5401.
ATL_V_TWR: AFA1900, Readback is correct, pushback and start up is approved, expect rwy 26L for departure.
AFA1900: push and start is approved, expect 26L for dep, will call for taxi, AFA1900

Set the altitude in your panel to 10,000, dial in 5401 (in the radio panel) since this is your squawk code, also in the radio panel dial in 116.9 for both comm1 and comm2) and set the nav course to 091.
Where did we get this from? the 10k and sq 5401 are from your clearance. The 116.9 and 091 are from your departure procedure. Look at the ATL5 departure chart. Notice that you will have to track the ATL vor outbound on the 091 Radial to fly to EATWO. Since you will be busy during flying it is best to set these settings while on the ground.
We also received our pushback and startup ... so do this now remember that you are expecting rwy 26L for departure, so push your tail to the south.

AFA1900: ATL_V_TWR, AFA1900 is ready for taxi
ATL_V_TWR: AFA1900, taxi to rwy 26L via Echo. (If you donīt know where taxiway Echo is, look it up on the KATL airport diagram itīs the twy parrallel and closest to rwy 26L).
AFA1900: taxi to rwy 26L via E, AFA1900
... a bit later ... you are now holding short of rwy 26L (Do not cross any runways unless you are cleared to do so! There may be traffic on that runway taking off or landing.)
AFA1900: ATL_V_TWR, AFA1900 is holding short (h/s) rwy 26L, ready for departure.
ATL_V_TWR: AFA1900, winds 250 at 6 kts, fly hdg 280 at the MM (middle marker) rwy 26L cleared for take off.
AFA1900: Copy the winds, fly hdg 280 at the MM, rwy 26L clrd for take off
... once airborne you will receive a hand off to the following controller in this example ATL_V_CTR
ATL_V_TWR: AFA1900 Contact ATL_V_CTR on 133.9, good day
AFA1900: Atlanta ctr on 133.9 good day, afa1900
Again go to SB, atc directory and double click on ATL_V_CTR, your comm1 will be set to 133.9 and AVC will change to Atlanta Center his voice channel.

AFA1900: Atlanta Center, AFA1900 with you climbing through 4000 for 10k (remember the intitial altitude you received in your clearance).
ATL_V_CTR: AFA1900, Atlanta Center, Radar contact climbing through 4k, turn right hdg 360.
AFA1900: Right hdg 360, AFA1900
ATL_V_CTR: AFA1900, turn right hdg 100 join the R091 to EATWO, c/m FL230
AFA1900: turn right hdg 100 direct EATWO, c/m FL230, AFA1900 ... a little later ...
ATL_V_CTR: AFA1900, Proceed direct GRD continue on the UNARM1 arrival and cross ADENA at 11k and 250kts.
AFA1900: direct GRD, cont on the UNARM1 arrival, cross adena at 11k, 250kts, AFA1900
(set nav 1 to 115.5 (GRD vor) and fly direct GRD, set nav 2 to 115.0 (CLT vor), once over GRD set the course to 047 and track it outbound to CLT.)

When to descend? A simple rule of thumb is to substract your cruising altitude in feet and drop the last 3 digits with the altitude you want to be level at and multiply this result by 4.
In our example we are at FL230 or 23000ft and need to be at 11k or 11000ft. So 23-11 = 12; 12*4= 48.
If you start your descend 48nm prior to Adena at a 'normal' descend rate of about 1800 feet per minute (fpm) you should be level at Adena at 11k. If you do not have an FMS or GPS how do you know when youīre 48nm from Adena?
Well on the Unarm1 arrival chart you have numbers between brackets below the bearings. Between Adena and Unarm intersection there are 7nm, between Unarm and GRD there are 35nm, so we need to descend 6nm before reaching GRD. Since 7 + 35 + 6 = 48.

Since the rest of the flight does not contain any 'new instructions or events'. I will leave you flying under Atlantaīs control to Charlotte. For charts of instrument approaches into Charlotte or any airport I would like to refer you again to Myairplane.com

An hour later you land safely in Charlotte, clear the active runway and taxi to the gate and set your transponder to squawk standby. (Always squawk standby when on the ground unless you are on a runway or told be ATC to do so.)
In the SB menu you should see Squawk Standby, when thereīs a checkmark next to it, your squawk is standby. At this time a controller wonīt be able to see your aircraft tag anymore. The advantage of this all is that when there are a lot of aircraft on the ground their data tags clutter a controllerīs scope. With squawk standby the controller keeps a clear view of the airport.

Remember that these controllers used to be newbies as well once, so ask for help if you need it, they normaly donīt eat pilots :-).
Also in case you didnīt hear or understand something correctly: Simply ask them to say again his transmission. For example AFA1900: Atlanta ctr, say again your last transmission for AFA1900 .

I hope this tutorial has helped you a lot and that you enjoy your future flights on Vatsim. Maybe we see each other during one of the weekly APG events.

Step 4: Additional Reading & Useful Links 

 Disclaimer: Not to be used for real world navigation. Author: Thomas Snoeck (VATSIM Senior Controller in Atlanta). I have tried to be as accurate as possible and to reflect VATSIM operations as you will most likely encounter them on this network. If you have any questions or comments please Contact me.