You might need to use DFSee to do the initial partitioning , I did on my workstation that has a 3TB main disk and three 2TB disks mounted in removable disk trays. I setup a 2GB HPFS boot partition and a 2GB HPFS maintenance partition ad use BootManager to select which to use. Other partitions are for Programs, Data, CAD drawings and specifications, and a catch everything else not defined partition, all of them being JFS.
You will also need the OS/2 you are installing to be updated with the latest fixpak and, if you have a subscription to Arca Noea, you might find some of the disk access updates helpful.