To determine support levels I look at the population once a year and decide by category of worker which of the two factions they'd be likely to support. Sometimes they all go one way, sometimes they're split 75/25, and rarely they're split 60/40, but more often then not it's a 50/50 to pad the numbers.
The factions themselves grow out of which officers (meaning all four categories) are doing a lot of work at the moment, as well as their personality traits. Those that do something particularly noteworthy get boosted to actually being a noble and placed on the council.
Basically any time I come to a decision, be it "What do I research next", "What do I build next", or even "which JP do I scout first" I ask myself "What would each side support here"? as well as "What does the Emperor think?" Then I act based on who has the most support, factoring in that one side doesn't ALWAYS get their way, even if that means doing something "stupid". The best example of this would be that some of the earlier, more pompous nobles tend to take a ship out for their own purposes on a whim, screwing with the overall plan. This will come back to bite them though (there's a bit of a spoiler in the chat forum if anyone wants to look ahead)