The maintenance partition can simply be another install of OS/2. Used to be some utilities that would create an maintenance partition out of your install. The one I used, bootos2, stopped working as the OS was upgraded. I'd advice 1-2 GB partition for it.
Partitioning, you need to use BootManager for multi operating systems. It needs a small primary of 1 cylinder, perhaps 8MB on your drive.
C: can be for DOS and Win3.1, a GB or even 2 at the most, partitioned FAT of course.
I usually put OS/2 on E:, a couple of GB's used to be huge but with stuff like the RPM stuff, maybe 4GB.
Can use F: for utilities and maybe data, once again a few GB or more. Things like MOZILLA_HOME can go on it and be preserved if needing to reinstall and shared if you need to use the maintainence partition, same with a lot of other programs.
Later if running out of room can add another partition of grow F:
About file systems, both HPFS and JFS work best with lots of empty space and can get weird as empty space approaches zero, so partitions on the large size are good.
JFS is likely your best bet for data, allows files larger then 2GB, journaling so chkdsk is much faster. Not bootable unless your using ArcaOS.
Backups are always nice. Now a days I use USB HD's partitioned as JFS. I have one partitioned as a 1 TB volume. Tried 2TB but with a lot of small files, chkdsk was failing due to lack of memory. These are USB3