@mr-johnson I would suggest focusing the Jedi/Republic side on a single capital ship (probably an Inexpugnable because a Hammerhead is still relatively small -- only 12 fighters, although the 400 passengers would be fine), so that they can move between various locations, which could them be built out of just 2-3 rooms as necessary (unless they're in orbit over an Indy world or something like that). I would suggest the same for the Sith when they come into play. If the Indy characters are all tied into the war in some way (and they really, really, really should be), then they'll have excuses to visit whatever world the Sith/Republic are over. You can also use Indy worlds (or slightly-behind-the-front-lines Republic or Sith worlds) for R&R periods and for RP with associated Indies.
There are definitely downsides to this plan (people tend to turtle up in their ships for RP and not branch out, but that's a culture thing that hopefully could be countered), but I think it's better than basing the "War Factions" on planets and then having to come up with excuses as to why they're involved in offenses across the sector/galaxy.
Whichever method you go with, I would strongly, strongly suggest focusing on a single sector of the Galaxy. I might suggest either the slice of space along the Hydian Way and just galactic northwest of Mandalorian Space (Arkania, Taris, Serenno, Yavin) or the slice directly galactic south-east of it, along the Perlemian Way (Feluccia, Rhen Var, Lantilles, Tanaab). Korriban and Dromond Kaas are right in between those two, as is Mandalorian Space.