My colonial nation's economy is in shambles. Despite that, they are still colonizing and paying for a ton of forts. Can I tell them to knock it off, or do I just have to subsidize them? Will they ever get back in the black? Is it better to subsidize them or pay their debts?
I don't think you can tell them to switch off Forts. I usually pay off their debts via subject interactions and help them with Influence Nation, which gives them extra MPs too. (Assuming you are a great power).
I guess you fed them too much land too quickly via conquests? If you pace your conquests, Colonial Nations are pretty good at handling themselves, but if you overload them with 100%+ OE, then you will need to help them stabilize, and yes they will be profitable once they core everything and bring down autonomy.