I haven't used my A1200s for years (and my primary one has a Power Flyer IDE adapter), but why not just set up the 4GB partition first (and leave the rest alone), get OS3.9 installed and working on that and worry about installing other file systems & patches and creating the large partitions?
That's what I did on my A4000 with an 80GB drive, then once the drive was partitioned (with SFS) I copied the whole contents from the 4GB FFS partition onto a 35GB SFS partition, changed the boot priorities and was done. I kept the basic install on the 4GB partition as an "emergency boot".
