There are two ways: the cache and dummy method and the baking method. The first one uses the upgrade bundler and has a short build time but a slightly longer install time. Should you ever have to rebuild your cache, you would also need to do this installation again. The baking method puts the upgrades and fixes right into the song files, takes a lot longer to prepare, but you won't ever have to rebuild your cache again.
I can upload the my original download of the files you'll need for the cache and dummy method, if you'd like to consider it.
For the baking method, as you can see below, you can simply drag the CON file to a song into the left pane of the Upgrade Bundler in C3 CON Tools and all of the upgrade files to the right half and click Bundle!
Do that for every song, pack them up if you want (another tool in C3 CON Tools takes care of that) and put them onto your USB drive, and if everything works, you can also transfer them to your internal hard drive on your 360.