you can safely run fp extensions on your site - however I would recommend creating a folder called say forums, and maing that a subweb. Go into that subweb with FTP (make sure both the FP and FTP usernamemes are the same) and delete all the FP items.
You can now FTP to that sub-folder without any issues - and edit the rest of the site with FP.
The two will sit happily side by side.
