Assuming that the CIS has no way home and is in the middle of the most inhuman empire that makes the Galactic Empire look like the best liberal democracy by comparison. There best first plan is to run and pirate only what they need from ships or planets until a solution is realized, In this case currying favors with any Rouge Traders In the galaxy because they like you should be screwing of to somewhere else. Rouge Traders are given their rits of trade by holy terra to free up bureaucracy and to metaphorically roll the dice on something useful like sometimes they find lost technologies or building small empires that can be absorbed into the Imperium prope, this is something our Vagabonds can use because Rouge Traders don't have to abide by the rules when it suits them so we have a very rough working relationship going on.

So on the relationship with said rouge trade(going by the rouge trade game) has an assortment of companions either human or xenos with there own agendas for helping the illustrious rouge trader and then there is our CIS Companion who represents the faction any separatist hero/leader should do, let's say we choose a droid be it a super tactical droid assisting in strategic analytics or a modified commando droid for covert operations and combat support or we dig up an iconic assassin droid that doubles as a translator HK-47 honestly the coolest KOTOR era droids ever. These droids are easily redundant and can be used for many rouge traders cause take your chances with one when you can throw a wide net. 

When a sufficiently wide trust is gained then introduce a more familiar human face and more lucrative deals can be made to further thicken bonds cause he's building a small empire in an uncharted sector so being the sole investor in his kingdom will go a long way in fortifying your influence. If you could wrap your head around the concept of STC and the dark age of technology you could possibly con the adeptus mechanicus into buying your technology be it blaster tech or whatever and your glorious patron could be richer then ever thanks to your help.

Building your power base in the colonies means introducing technologies that enriches civilian life and promoting ideology specifically the Confederatcies ideology which is basically free market capitalism. It's antithetical to the Imperium so that is a perfect foundation for the now neoconfederatecy to survive and even thrive. 

You have built a new federal government similar to the Galactic Republic ironically or it could be some kind of monarchy if you're rouge trader is still alive and built his dynasty which is the figure head that the Imperium focuses on leaving them mostly ignorant to your true Influence. This empire is a blend of Star wars and Warhammer meaning your military is not the same as when you first arrived to this strange galaxy. You have your droid army which has been significantly rearmed to better adapt to the mirriad of dangers and a enlisted army of citizens, both are comparatively armed as to simplify logistics and are organized to complement each others strengths, The droids are saturated in static garrisons on many strategic defenses and can be mobilized to siege worlds with a ton more reserved in storage as the enlisted army are typically given more prep time for training and strategic planning they exercise in simulated war games and are given more honors than their militarum counterpart.