You don't say which release of Rockbox you are using, nor which model of iPod. Would need to know that before someone could advise you.
In general if the ipod is booted into rockbox when it's connected to the PC, I don't think iTunes will recognise it as an iPod. In any case you won't be able to use iTunes to sync, you'll have to copy files across with drag-and-drop, including the playlist files.
Or you could use a different music manager like foobar2000 or media monkey or something, for organising and creating playlists. You _might_ be able to sync with those, not sure, depends what plug-ins they have for that purpose.