You're doing it the wrong way - the OS/2 boot manager must be put in first, and OS/2's fdisk used to partition the disk.
Note that none of the operating systems you mention can handle disks that large without updated drivers.
Disk layout :
Primary - OS/2 Boot manager (probably about 10MB, depends on geometry)
Primary - FAT16 - MSDOS/Windows 3.1. 2GB.
Extended - OS/2 HPFS boot. 400MB. Doesn't need to be any larger.
Extended - NT 4 NTFS boot. At least 500MB, a GB to be safe.
Extended - FAT32 (Win 98), whatever you want. Can't remember '95 limits, probably a driver to increase them.
Extended - NTFS
Extended - HFPS - OS/2 data. 20GB will handle any OS/2 app you care to mention, unless you're heavily into graphics.
Extended - more FAT32 if you want it.
Make sure that whatever size the OS/2 and NT boot partitions are, that the OS/2 boot manager offers the option of 'set installable' when run from the install program. This ensures the partition is entirely within the first 1024 cylinders and bootable.
DOS and OS/2 boot from their own partitions. NT 4 boots partly from the NTLDR files it will stick in the DOS partition, and partly from its system partition. Windows 98 will put some files on the DOS partition, and some on its install partition.
Order to install : 1) OS/2 boot manager. Optionally also OS/2. 2) DOS 3) Windows 3.1 4) Windows 98 5) Windows NT. NT will disable the OS/2 boot manager, it will be necessary to use an fdisk program to set it active again. There are drivers for OS/2 and NT that will handle large disks, these can be applied at install time, or after installation.
My retro system has at least DOS, OS/2, Linux, and OpenBSD on it. Can't remember what Windows versions I put on, but will check tonight.
Technically, yes, you can dual boot OS/2 on a FAT partition with DOS. You really, really, do not want to do so.