Using HD Driver to create Fat32 Partitions wont make them Windows compatible.
Use Windows for that
But if you do, you cannot use more than one partition on the disk.
So, your IDE Drive, to make things as simple as you can, only have a few TOS and one LNX partition, and the SCSI Drive, chuck into a PC and partition it as FAT32 thats the whole drive... It wont work in normal Atari/TOS Mode but it will be a full 10GB Partition that both Windows and MiNT can use.