If it's just loose boards, you can nail through the carpet. There are even special screws, whose name escapes me, for that purpose.

Of course, to really find out what's going on and repair properly you have to remove the carpet.

When we replaced our kitchen vinyl floor, the floor was uneven in one place because of an old leak. To correct the problem, the damaged part of the floor was removed and replaced. Then a new, thin subfloor was installed throughout the floor. I forgot what they call it. It's sort of a thin plywood made specially for that purpose. Floor dealers use it all the time.

If your floor problem does not involve water damage, you probably will not have to replace any damaged part. Just cover it with that thin plywood, and you'll have a nice smooth surface. Then you can lay whatever finished floor you want over that -- carpet, wood, etc.

If you want to fix the problem, you really need to find out what is wrong. A squeaky board might be fixed with a nail or screw. A structural defect may require considerable effort and expense to fix. Minor damage can usually be addressed relatively cheaply if you are in the process of replacing carpet. We (and you) aren't going to know what it entails though until you find out what is actually wrong.