I name each system I have planets in differently, so my Homesystem the planets are <System Name> Prime, <System Name> 2, etc till I've named all the planets. When I set up a colony or outpost in a new system I give it a new name and use the same naming scheme, prime for the first colony or outpost I set up, then 2 through whatver for the rest as I go. Currently, I've been stealing the system names from Starbase Orion :P