So there is many steps to take when going about this, but as long as you claim that third base; it should be effective, here they are:
Create a transport system between the bases:
You can find some other players who are willing to help you if you want, but creating three bases and having a very well organized transport system that goes through all three would be a good place to start. Create an underground system, of track that takes you in and out of each base; especially if you plan on building a large city.
Organize each base:
A good place to start when maintaining these bases is to have specific things in each of them. For instance, one base has building plots and homes. Another base sells weapons, armor, redstone, blocks; you name it. The third base can be something like where you farm your wheat, and have nether portals and mob spawners.
Have a centre, or hub
I know it's factions, not towny. However, having a nice center town area where members of your base could potentially trade each other items. Whatever, but a good center place is a good place to branch your bases from.
Build your bases strategically
You claim you are gonna be a hermit, so I suppose that means your gonna be more on the defensive than offensive side. Build your bases at places away from enemies and closer to allies.
Find a place where a lot of people come across, as well; so you have more people to recruit to your faction.
Just because your base is organized, doesn't mean it's fancy. You don't need gothic cathedrals; just designated space, even underground to build each of your basis. With the exception of the houses, considering you want them to look nice.
Maintaining bases can be difficult if you're trying to prevent being raided by someone else. You have more space to help protect. Try to have good pvpers that belong to each of the bases in case of a raid by your adverseries.
This is just my silly opinion, so take it with a pinch of salt. That's just what I would do. If you agree and find it works for you, amazing. If not, well then don't take this post too seriously.