installing in public folder

I will be installing this through Fantastico. I currently have a CMS installed in the public folder. It is not in a folder of it’s own. I would much prefer to do the install of WP in the same manner/ same way. Is there anything I should be aware of that may cause problems with this? Could I have a problem with a file that is named the same as a pligg file? I presently have Pligg in this public folder, and running.