Let me sum this up as best as I can, using the large fleet vs fleet scenario:
Vasari:
Stilakus Subverter: Around 10 or so of these. Keep them close to the front lines, spread out from each other. Micro them to get close to the packs of enemy ships and let them do their jobs.
Overseer: 2 to 3 at most. Make sure it is the ship you have least of. Keep them close to your most critical ships and when said ships get critically damaged, micro time.
Advent:
Guardian: Get about 6 of these in a spread out formation, and when the enemy opens fire, they will automatically use their abilities.
Domina Subjugator: This ship can be very powerful if in the right hands. It can disable ships for a considerable duration with some sort of ability. Use 2 to 3 at most against the enemy's most critical ships.
TEC:
Hoshiko Robotics Cruiser: Get a decent bunch, roughly 1 for every 4 to 6 other ships in your fleet and let them do what they do. Make sure Demobots are researched!
Ceilo Command Cruiser: Use 2 or 3 of these. Embolden doesn't really do much when a ship is under direct fire, I've noticed, but Designate Target, as stated above and proven by me and the expierenced player, works wonders against Starbases and Caps if you have LRMs, Ogrovs, Bombers, and don't forget the Marza Dreadnought.
Enough said.