Re: CSS files. . .
Yes, please keep your modifications restricted to files in the template folder. If you think you need to modify something outside that folder, it’s probably already possible with a plugin. If it’s not possible with a plugin, you’re getting into modifying the bbPress core, which is a very bad idea for keeping up with new releases.
I recommend copying all the stock theme files over to a new theme and then modify those files. That way, you can always refer back to the original if you break something, or you can even revert to the stock theme if you really break something.
Or this more recent explanation: