One method you can try is to use the Rename Move and Copy tool built in to Media Center. If you already have the files from the USB drive imported to the library on the Id, you can use this to move the files onto the Id's hard drive and update the database to point to the new location all at once.
I would suggest trying this out with a couple of files first, to make sure you get the results you're looking for. To do this, select a couple of files, then go to Tools -> Library Tools -> Rename, Move, & Copy Files (or just use F6). Select "Copy and update database to point to new location" from the drop down menu at the top, then check the directories checkbox. The default path is usually /home/media/Music which is fine, then click Ok. Then you can check to see if it moved the file(s) to the Id's hard drive and make sure it still plays. If everything looks good, you can repeat the process with the rest of the files. You may want to do it in batches instead of all at once. The Id will probably seem like it's frozen for a while as it copies the files.