I have just added a 2TB Seagate SATA drive to my A1200 with FastATA/Sata adapter, OS 3.9
The first problem I had was with OS 3.9 HDToolbox.
I recommend first installing the RDB with AmigaOS 3.9 BB2 HDToolbox. Once the RDB is written, do not add partitions yet as soon as you press the PARTITION button, HDToolbox attempts to automatically add hundreds of small partitions which eventually crashes the Amiga!
Go into HDInstTools, manually add a few parititions at the start of the hard disk, then save and reboot. Go back into OS 3.9 BB2 HDToolbox and resume adding partitions (no crashes this time)
I recommend using SFS1 v1.279 for the System partition (bootable) and SFS2 v1.279 with long filename support for all others. Keep the first bootable partition (System) under 2GB in size.
You should ensure before prepping the hard disk that you have a patched 64-bit scsi.device and 64-bit Filesystem to use on the hard disk.
Hope this helps!
