Ah I figured it out. But thank you Seleuceia for steering me in the right path.
Sorry, I should've first stated I was working on the GSD for a different mod. For those wondering what they need to do, you have to go into the original GalaxScenarioDef file in the actual "sins of solar empire rebellion", find/scroll down till you get to the part that says:
planetItemType
designName "Psi:CapitalShip:BattleShip2"
entityDefName "CAPITALSHIP_PSIBATTLESHIP2"
(thats for the new Vasari Cap ship), open the GSD file of the mod you're working on, find/scroll down to the section that says: "planetItemTypeCount", add three to whatever number is there (3 for the 3 new capital ships), and then insert in the sections (like the one I showed before) in line with the other planetItemType passages.