There are a load of procedures you could follow, just search around you'll find quite a lot.
I recently did the same move you are looking to do and I had no problems. The complexity is down to the size of your data. Also, when backing up to desktop, make 100% sure that you verify the file. That is really really important.
One thing I wished I did may sound convoluted, but it makes sense.
1. Backup ibays manually.
2. Delete ibays
3. Backup to desktop
4. Verify
5. Restore on new server
6. Re-create ibays manually.
7. Restore ibay data.
The backup process does save the ibay data, but if you have a lot of files and scripts in your ibays, it can take a while. My backup file was only 560 meg, and half of that was just Ibay data. The backup/restore process took, easily, 5 hours to do (though my server is a poky 600 mhz).
Anyway, search around and find the process you feel most comfortable with.