The common method for something like this is an X-pen. Put the dog in a room in it's crate. Then re-arrange so the dog has a foot of the room that it can explore outside it's crate. The re-arrange so it has two feet (or three or four or whatever you're comfortable with). The idea is the area keeps expanding until the dog views the whole room as it's den. This is kind of difficult to do in a basement area though.
You've cleaned the spots with an enzyme cleaner I assume?
You've cleaned the spots with an enzyme cleaner I assume?