just use the command to upgrade like this:
db3_upgrade *.idx *db
That would run the command on any .idx and .db files in your current directory. I know that command is not right, but I don't remember off hand the berkeley upgrade scripts.
Once you've got your database upgraded, do your self a huge favor, and use the tools MT provided to convert your database into mysql. It's not a hard process really, and it will save you headaches. You don't have to upgrade mysql databases with every upgrade, and it's more secure. Ditch berkeley, it's just plain smelly.