Tag first, send to emplode later.
If your ripper doesn't fully (and completely) tag your music, then you're using the wrong ripper. If you're downloading all those songs from the net, then consider buying some CDs and ripping them yourself.
MP3 Tag Studio is one of the better batch tagging program for Windows. It will NOT allow some of the advance management tag methods of emplode. Tag Studio is file-based, where emplode is tag-based.
Another way to pull music off the player is to use FTP with Mark's Hijack kernel installed. Of course if your music isn't tagged (ID3) you're going to be screwed having only the FID# as a filename.

Using MP3 Tag Studio you can rename a batch of files from the information in the tags. Catch 22 for you probably.
Emplode will do a basic naming job on files you save back to your PC, based on the PLAYER tags. You can then run MP3 Tag Studio and do a FILE NAME to ID3 tagging operation.
Filling in tags for loose files is a pain in the ass. You should probably look at MusicMatch for looking up individual tracks (you need some basic info for it to do a search).
If this is indeed all music you have on CD, I'd re-rip the entire collection (with a good ripper that supports FreeDB and ID3V2) rather than play around with all that file moving and manual tagging.
Good luck.
Bruno