I assume that when you say you're cleaning up all the MP3s using the software, that you'll need to upload them all again to the player.
Depends on what you're trying to do.
The whole idea of using a product like MP3 Tag Studio is to clean up the tags in the collection on your PC. Generally, you should do this BEFORE you send the files to the player in the first place.
There isn't any way to edit the tags with 3rd party software while on the Mk2?
There isn't any way to edit the tags PERIOD on the player at all. The tags are not touched once they're in the player.
You're perfectly welcome to rename things with Emplode once they're on the player. With the 2.0 release, there are actually some pretty nifty renaming features in Emplode.
The only problem is that Emplode only edits the player's database. It does not edit any actual MP3 tags. It does not write the changes into the MP3 files, either on the player or on your PC's hard disk. It's just changes fields in the player's database.
This is why many people are asking for utilities to help them. There can be a discrepancy between the tags on their PC and the database entries on their player. MP3 Tag Studio won't help you synch up your player and your PC, but it will help you get things right the first time before sending them to the player in the first place.