Any Amiga with lower OS than 3.9 cannot recognise hard drives more then 4GB (I don't remember about 3.5), so even if you install a 40GB hard drive into your A1200 with AmigaOS 3.1, you will have only 4GB.
Also consider that if you want to install OS 3.9 you must have Kickstart 3.1 (A1200 comes with 3.0 version), and ensure that the first partition (the boot one) doesn't exceed 1 or 2GB else you will have problems I think. The other partitions can be formatted as much as you want.
... and welcome, it's glad seeing people after 10 years or so, rejoin our community. ;-)