We have launched 35 satellites, and have quite a large base. However we're now running into resource bottlenecks and realizing we need RSO. We didn't start with RSO though. If I apply RSO now what will happen? Will it change the map we already have generated? Or are we too late?

If you just add it it will start working in newly discovered areas. I think - didn't test that variant.
You could add it and then use regeneration - that would respawn everything through the map except starting area. And would require to use /c command. It also respawns biters so results are usually interesting.

Thank you for your response! I think we're going to go for it. I'll wait till the whole team is available to fight off the biters!