I admit I don't know what "3u tools" is.
But surely you can just copy the existing audio files from it by connecting it in disk mode, doing a wildcard search for the various audio-formats that might be on it (*.mp3 etc), and drag-and-dropping the files to the computer with Explorer (or whatever the Mac equivalent is). They'd all have the obfuscated-nonsense filenames that iTunes gives them when syncing (assuming it was originally synced with iTunes) but you can easily recover the correct names with your music manager if they have been tagged correctly. (If they haven't been tagged, then you'd have to listen to them all and recognise what they were, and fill in the tags, and rename the files, and reorganise them in album folders 'by hand', which could be quite tedious).
The best way to keep the existing files, IMO, is to copy them to the PC as above, then after you've installed rockbox, copy them back to the ipod again (hopefully after you've correctly renamed and folder-organised them).
If you keep them on there as they are you'd have to make sure you created rockbox's database (again, assuming the tags are filled in) as the file names would all be the usual apple nonsense so you couldn't use the file-browser. Not sure you can keep the files on there from before anyway as the process of installing rockbox might mean you have to reformat/restore the thing - I guess it depends on whether it's a Mac formatted or windows formatted ipod?