You can use any program to manage your media for Rockbox because rockbox creates it's own database that's independent of the actual directory structure, so any utility that can somehow sync it's Music to a flashdrive works with rockbox (you could even sync your library with rsync or unison).
Banshee (http://banshee.fm) is a nice, but sometimes unstable and buggy, music manager with nice UI and features like maintaining a directory structure based on the metadata of the music, managing podcasts, plugins for LastFM, Amazon etc. Managing Videos. Banshee even has special rockbox support (rockbox is detected via the .rockbox directory) but this only works if you delete the directories created by apple (
ipod_control etc) otherwise it will be detected as iPod. When using banshee keep in mind that it can't embed Covers into music files but stores the covers in
Other nice programs are Rhythmbox and Guayadeque. Rhythmbox has many of the same features as Banshee with a clean UI and Guayadeque is much less user friendly but has many nice features, of which the custom copy feature is the most interesting for Rockbox because you can specify in what directory structure you want music to be copied.
But see for yourself, you can easily manage the same directory of music with all three applications at the same time, so don't be afraid to try out all three.