Yeah, basically you can either partition all your cartridges the same with HDToolBox, OR you can create a mountlist for the drive and work with them that way.
If you had to ask, then opt for the mountlist. If you create RDBs on them with HDToolBox, you really need to know what you are doing, as if you insert cartridges with different RDBs in without a reboot in between, you sometimes end up with interesting results.