Okay, so I created a custom map with 3 factions. The first was my desired faction (called "Terran Federation"), the second, a small enemy faction (called "Terran Seperatists") and a third larger enemy faction, caleld "Vasari Imperium"). The first and second factions' homeworlds are in one star system, while the third is in another entirely.
I planned on playing as the Terran Federation faction, but ended up as the Terran Seperatists, or at least my homeworld was the one I set for them.
My question is, how do I make sure (or set as I start the game) that the Terran Federation faction is "Team 1" (the default for the user)?