Bluehost How-To : FTP setup in Dreamweaver 8 - confused

I have a BlueHost site (http://www.mistywindow.com) with 3 sub domains and 1 add-on.
Everything was created and published in FP 2003.

I wish to remove FP extensions from the main and subsites on my server and be able to publish using FTP with Dreamweaver. I’ve cleaned up the HTML in preparation.