Firstly, yes the files with '~~' in the name can safely be deleted. But, no matter what you do, like weeds they'll come back again :-(

I don't think .obj files will show up in the browser. They need to be .vob files to do that. But you can load up the .obj files, assign the materials as required, then save them out as .vob files. Then you can see them in the browser (and they'll be faster to load, too).

Steve