Am not sure exactly what kind of clean up you are trying to do. But in the WP dashboard under SETTINGS : Site address (URL). this would make it possible for you to keep your current install with it is while making your WP site url www.mysite.com , which seems to me the best of BOTH worlds. As far as deleting your site builder files, well that you'll have to do manually. be careful not to delete any content that you have linked to your WP site directly.
Your OTHER choice would be, after deleting the OLD site builder files, to move the WP files up one level as if you were transferring them to another domain. [URL="http://yoast.com/move-wordpress-blog-domain-10-steps/"]A great step by step guide can be found here
IN either case.. if you have made "pretty URLs" for pemalinks you might have to fix those manually.