Can you explain a little bit more what you mean by "acts strange skipping sometimes"? What skips? portions within the track? or skips to a next track? I haven't notice any of this problem with Rockbox on my 60GB iPod.
Also.. you can use whatever program you want to put the songs in the ipod. You can even drag and drop the files and put them in whatever folders you like, the way you like it best organized.
You can still use Itunes and Rockbox but then you'll have to use the Database to play the songs.
Take a read of the manual so you can see all the possibilities!
Ben