I don't think you need to clear anything with the SCSI2SD (unless you want to adjust that drive layout to be a single unit and use partitions from the Amiga instead). Just edit the tooltypes in the HDToolbox icon to use gvpscsi.device, (re)prep each "drive" with an RDB, partition to your liking, and you should be set.
Edit: also, for now, set the boot priority of SDH0: to 1. If that's your main system partition, you want to make sure it boots first. If all the partitions are set to priority 0, I think that's why you're getting the boot problem you described.