I have no experience with Muse, but from its description it sounds like a WYSIWYG site builder in the vein of FrontPage/Expression Web, Dreamweaver, CoffeeCup, PageMason, etc. If you have an existing site, you should probably be on the safe side and completely remove the old site, so that there's no leftover junk that might interfere with the new site. Other than that, I presume that they include instructions for how to upload to a hosting provider such as LP.
By the way, you will not be uploading "to" FTP. FTP (File Transfer Protocol) is just a method for moving files between your PC and your hosting (site). Muse will need your server address, account ID, and password, and should be able to take it from there.