When you click on the Starbase tab you will see the same project list that we've seen the past few months (wow can't believe it has been a few months already). When you click on the Embassy tab you'll see a similar window except for the Embassy. If I recall correctly there are only 3 project slots. Two regular and one special. I could be mistaken since I'm not in the game right now to look at it, but I'm pretty sure that's how it is set up.
Each one works independently from the other, so working on the Embassy won't slow down progress on the starbase. What is also nice about this is that we will be working on more projects at the same time which means players will have more opportunities to earn fleet credits.