The Separatists in this will be a faction in the Republic which is made up of systems that wish to join the CIS, for political, economic, or other reasons.
You could be a commander of either a CIS ship/ fleet or a Separatist planet's ship/fleet if you want.  There is a CIS droid control ship at Naboo, but it is civilian.  It is there to introduce droid workers to Naboo's factories to get the leaders of industry to join the Separatist movement on Naboo.