How much money are you making? How much do you think you should be making? In the current version of the mod it is very easy to get a regular income of 10k+ if you've properly developed your planets and your economy though it does take a little bit of planning.

The Republic has an advantage since it owns most of the core but even the CIS is pretty well positioned to take some high income planets and valuable trade port worlds from the Republic as well as integrating member state planets to develop to your own ends.

In my experience, building Tax Collection buildings on high value planets is essential. Look at your various planets and see their base income, if it's over 200 credits, that's a good candidate for a tax building, 300 or more is a must, don't be afraid to have a low Influence score on them, as long at 4 or above you're safe. Having a high infrastructure score, and factory buildings reduce the ship upkeep. It's only a tiny amount but since you'll want factories on your planets anyways for defensive purposes, but it can help offset the upkeep by a significant amount, it also helps if only to keep the cost of units down. In addition, building Trade Hub Stations on systems with a lot of connections is also a good boost. 50 credits per connection may not sound like much but I find it all adds up fast, especially on planets with the Trade hub boost.

Early on, try to prioritize systems with the ability to build mining stations, many of them also have a high base credit rate so you can easily rack up roughly 1000 credits from them.

As for building up your forces early on, don't be afraid to depopulate some systems of both ground and space forces to build up your initial fleets and armies. They may have a hodge-podge nature to them with several units that don't fit your playstyle but they can nevertheless be strong enough to go on the offensive early on and seize those valuable planets to further boost your economy. Your Heroes especially will be useful in boosting your early-game forces, I'm currently playing the Separatists and I found that Grevious and Trench are powerhouses in space with their improved ships and passive boosts, and Dooku, Sora Bulq, and Ventress can decimate almost anything on the ground together.

You are limited early on, yes, but you also have the means to get the ball rolling, it's just a matter of hitting the right places early on and building them up.