Quick tip: You can specify absolute urls in tinyMCE quite easily.
document_base_url : "http://yoursite.com", absolute_urls : true
I am sure this is an RTFM but I did not see anywhere exactly where it was. I have been using this with the ajax file manager and it seems to be working quite well. Interested in other file managers in TinyMCE check out tyssendesign.com.