Why in the heck are you using such a large HD? Is it the only one around you've got or something? To maintain the highest level of happiness without all this patching nonsense in 3.9, stick to a HD that's 10GB-20GB in size and partition it logically considering the built in filesystem you're using:
80mb-500mb for AmigaOS and 4gb-8gb-12gb-16gb for your other partitions. Just a suggestion as that's what I do for work:, programs:, utilities:, games:, etc. No way in shitsville are you ever going to fully utilize all that space you have now. Amiga programs and files are simply NOT that large! lol