No problem.
I have only flown the aircraft in the Single Missions, you just select them from the drop down menu like the normal ones. I haven't fiddled with the campaigns yet, and I don't think the sim will load them for Instant Action. As for multi-player, well, it'll have to wait for HyperLobby.
The loadouts can be changed just like the normal aircraft, and the weapons will all reflect the actual aicraft. MiG-21's will use AA-2 Atolls, and O-1E's can mount HVARs, etc...
If you want, I can send you a modifed *.ini so you can directly see the changes, but it is exactly like I described it before. There really aren't any suprises or difficulties.