If you use the database and select an album it should show the tracks in that album in the correct order, unless you are using a custom tagnavi config file.
For changing the filenames I'm sure mp3tag can do bulk renaming, but you'd have to read the documentation of that utility for how to do it (I can't remember offhand..,oh, and force it to use two digits and maybe also the disk-number if it's a multi disk album). Also whatever music manager you use could probably do it as well...in fact would be better that way, come to think of it, because if you use mp3tag your music manager might then get confused by everything having changed.