Boot Manager's partition must reside within the "FAT Barrier", that is, below cylinder 1024.
DOS and OS/2 bootable partitions, whether FAT or HPFS, must also reside completely within the FAT barrier.
DOS-compatible FAT partitions must reside completely within the FAT barrier (no surprise).
OS/2 non-bootable HPFS partitions can go anywhere and be any size up to the OS/2 limit of 512 Gb.
Allocate Boot Manager as the first partition (lowest address) on the drive.
Next, if desired, allocate a DOS boot partition (possibly with space for MSWin as well).
If desired, and if the DOS boot partition is relatively small, add a second FAT partition for use by DOS and MSWin when RealDOS (PC-DOS or MS-DOS) is booted.
Allocate your OS/2 Warp boot partition, either as FAT or HPFS.
All of the above must fit within the "FAT Barrier".
Finally, allocate the rest of the drive, however large, as one HPFS partition.
If the drive performs the translation, it should be transparent to the BIOS, DOS, and OS/2. If the adapter chipset performs the translation, the same will hold true. However, if the translation is performed by the adapter <BIOS>, problems can result unless the manufacturer also provides an OS/2 driver for the adapter or OS/2 uses the (slow) IBMINT13.I13 driver to force all disk I/O through the adapter BIOS.
There is an error in the Warp User's Guide on page 310. It states that "Typically, the first 1024 cylinders is equal to 1 GB (gigabyte), or 1024 Mb." More frequently, 1024 cylinders is 512 Mb or so, but it all depends on the drive manufacturer. I believe that the statement in question was the result of a mis-condensation of a comment made in the OS/2 v2.0 Control Program manual referring to <IBM> drives; in any case it is incorrect.