First off, you won't be able to install FreeBSD on a FAT32 partiton. It will have to be some other sort of format, probably available through a formatting tool with BSD...

Usually *nix, in my experience uses something like an "ext" or "ext2" format. Although there are dozens if not hundreds to choose from.

Keep in mind that depending on the install features of BSD (I've never played with BSD so I dont' know), but it should lead you through formatting and partitioning the drive.

I don't think PartitionMagic will format the drive how you will want it anyways... regardless, don't forget a swap partition (approx. the size of your available RAM), root partition '/', and then whatever other partitions you might want... I usually just throw everything else in '/home'.