Yes, you can give the capital ships waypoints and orders in FRED.
But in game?
...no. Probably not. I mean, you could make a mission where you ordered capships around, it'd probably just be awful.
If it's anything like FS2 (which in most ways it is), capship combat is best handled by preset waypoints and careful scripting. The capital ship AI is not meant to work on its own. A base ship, for instance, would get as close as possible and begin circling its target (which makes very little sense.)
In any case, in what possible situation would a Viper jock be giving attack orders to a capital warship?
You might be able to give the Bolitho sensible attack orders, but not much bigger.
However, the ships will certainly be PRESENT in single and multiplayer missions. They'll shoot at the enemy, shoot at you, shoot at whatever you tell them to in FRED. They'll move around and follow their courses, you'll be able to blow off their turrets and disable their engines, all that. You just won't be able to tell them what to shoot or where to go in-game.