1. don't know. I am not sure about the bonuses stacking. Design question:
2. don't know. However, a one ship fleet is permitted - so to be sure - put the ship in its own fleet. I do this with relic ships anyway so I can access them from the fleet management screen.
3. As soon as I get fleet ECM, I design a small number of "FLAG" ships. I design them to be slightly more maneuverable, and more heavily defended than line ships. I name them "FLAG" (in caps) so I can see them easily. These ships get the fleet wide ecm components - line ships don't. FLAGS also get the first fighter wings when available (long before carriers). I usually assign one flag to small squads of ships (6 and under), and to flags to larger fleets. My admirals get relocated to a flag. Flag tactical doctrine is to stand off against stronger and weaker enemies. The only exception to this is when I have a relic ship that is much stronger than a flag - then admiral goes there. In early game, some relics have fleet ecm before I have researched it. In this case, the relics are used as flags, for larger fleets only,except when I need a large, quick massive strike, then relics go into their own fleet to get use of maximum speed, etc.