What problems are you experiencing?
Loading the files onto the iPod is no problem, but slow of course. I only use the Apple firmware for this. Updating the database does take a very long time. I currently have around 62,000 ALAC songs and when I add a few more it takes days to update. I leave the iPod plugged in while this happens. I need to look at the options for updating specific directories.
There is a 'cache directories' option in Rockbox, which I think is intended to remember where new files have been placed. However, I assume that only works when using Rockbox to copy files.