It depends on whether you leave your ships automated or not.
If you leave automated on, Escort class ships tend to do escort missions to a freighter (and waste loads of fuel whilst they are at it and not protecting anything much and other Empires seem to get angry at you for having escorting ships in their territory.)
I think Frigates split themselves between escort missions, with a tendency to escort construction ships, and forming fleets, with an empahsis towards the smaller strike fleets, if you have left fleet automaton on.
Destroyers and above tend to form fleets. Cruisers and above always join the larger main fleets.
My memory isn't too clear since I don't normally leave automaton on. So this may none of the above may be true.
There are no bonuses, or design restrictions to any of the military ships (except the carrier and resupply ship). You are free to design them whichever way you wish, and use them however way you wish, if you have turned automaton off.
One thing to note, is that naming of escorts, frigates and destroyers are different from the other ships, so they are much easier to find them. In fact, I use their naming as a way to find new ships.
< Message edited by Plant -- 11/19/2013 11:32:16 PM >