To be any real help I need to know a few things,
First, when you say multi-file do you mean one html file and then all of the attachments (pdfs, images, etc.) are separate files? Or do you mean each tiddler is it's own .tid file?
And second, how are these going to be hosted? If it is a situation where you copy the html file into a folder and then it is accessible at some url than it should be relatively simple, if it is some other setup than it depends on the specifics of the setup.
And finally, how are you putting the files in your wiki while using Bob? Are you dragging and dropping them in the wiki or are you using _canonical_uri fields?