Log into the Control panel and go to your DefaultGame.ini file and enable PB, then select the /Binaries/pb/pbsvgame.cfg file to edit, and place a 1 where the sv_punkbuster 0 is for the punkbuster.
This will enable it for your server, then just restart.
The servers are ready for PB to run keep in mind the client will need the latest version to join the server though.
Here are some tips on how to set it up:
If the server is up to date then the client will auto-update to the server's updated version. However, if the client is newer than the server then it won't force the server to auto-update.
One alternative that may (and should) work to update the server to the latest version:
Execute "pb_sv_update" using the AdminPBExec console command from a client to the server may be a way to get the latest into the server (but make sure the server's pb directories and files are not write protected). If you cannot join with your admin command try disabling PB in the configuration file and then joining the server as an admin. Then execute the pb_sv_enable followed by pb_sv_update.
Here are some other tips from our friends at Airdale ops:
This is an announcement to all America's Army 3 Players...
The Server Administrators for America's Army 3.x are looking to turn Punkbuster on for the servers to get the protection and control they need for the servers to keep the gameplay the way it is suppose to be.
For the Server Administrators to turn PB on, all players must manually update Punkbuster on their PC otherwise when you join the server you get stuck on the Team Selection and will not be able to play, then a little bit later you are kicked back to the browser.
Please follow the instructions below immediately to avoid having such issues when Punkbuster is finally enabled on the servers. Yes, you do need to do this as very soon most servers will have Punkbuster enabled and you will run out of places to play otherwise.
First download and install PBSetup from the following location:
http://www.evenbalance.com/index.php?page=pbsetup.phpOnce you have downloaded pbsetup just run it from any location and click "
Add a Game".

Depending on delivery method and operating system it will be 1 of 4 paths. When you click "Add a Game" the path found is incorrect so you must browse to locate the "Binaries" folder,
DO NOT SELECT "pb" folder as it is created or overwritten.
Paths are as follows
Deploy Client:
x86 (32bit) Windows
C:\Program Files\USArmy\America's Army 3\Binaries
64bit Windows
C:\Program Files (x86)\USArmy\America's Army 3\Binaries
Steam Download
x86 (32bit) Windows
C:\Program Files\Steam\steamapps\common\america's army 3\Binaries
64bit Windows
C:\Program Files (x86)\Steam\steamapps\common\america's army 3\Binaries
Again, make sure you have selected the Binaries folder and NOT the pb folder.

After adding the game, click on "Check for Updates".

When in-game, users will also need to click "Enable Punkbuster" on the MBS page America's Army 3.

Further support for admins and player can be found at www.airdaleops.com