I don't know what the the heck I'm doing wrong, but I'm having issues creating fleets. For personal preference only, I usually like to make a cap ship my fleet leader. Let's say I've a few frigats and some cruisers already built, and then I build a cap.
1)I've tried designating the cap as a fleet leader and right click the auto join on. But only ships being built AFTER the cap was, will auto join.
2)I've tried moving all ships, with non marked as leader into a small area, then making a box around them by dragging left key and then clicking on create fleet button. This will randomly make any ship fleet commander.
The only thing that seems to have worked for me so far is making the particular cap the fleet commander and then sending any misc ships to a nearby astroid or planet, turn auto join on the cap and then sending the ships back to the orginal planet where I'm building a fleet. This is VERY time consuming! Especially when you're trying to create a fleet out of what's left over from two or more fleets that just seen battle and have had losses.
Again, this just personal preference. I don't think the AI understands or makes use of a fleet structure as we would in real life with the command being on a major platform directing the combat actions of lesser platforms. Such as miltaries make use of aircraft carrier fleets today.