RyanR

In the air. A-10 pilots would sometimes use other A-10's, per an article on the internet.... somewhere. While ground boresighting kinda works in DCS, IRL Mavericks drift during takeoff and when pulling G's. 
IRL, I'm sure pilots are briefed on suitable places to boresight (a town, for example). In DCS, this gets tricky since Mavericks may not "grab onto" a static map object, so that would effectively break the mission. In the ME, it would be best to build a little area near a town to boresight on the way to the AO.
-Ryan

Two different weapons systems, really.
Just turn JDAM's "on".... they'll be happy when you need them. The sensors on the plane get the GPS coords, and then send that to the weapon. The bomb now knows where it is and where it needs to go.
Mavericks care nothing about GPS coords. They technically don't even care about what any of the onboard sensors tell them. They're optical. They chase an optical target that you tell them. You absolutely have to boresight them to the targeting pod, which ultimately also aligns them to the HUD to make them easier to target when things get hectic.
So, yes, turn on the weapons, and they will do what they need to do in the background. Just remember that Mavericks need boresighting when they come up.
-Ryan