OS/2 needs to know which drive it is booted from. The standard way is to install BootManager in a small primary partition using LVM. You could chain boot it from your Bootman, I've done similar with Grub, or use it to boot all OS's. The newer way is to install AirBoot into the MBR, which would break your Bootman.
Understand that OS/2 is picky about the partition layout, it has to be CHS partitioned (unless using the latest ArcaOS) and the way for OS/2 to co-exist with other operating systems is that all partitioning has to be done with OS/2 tools, LVM with Warp 4.52. during this process BootManager can be installed and the OS's can be added. Afterwards you can use the other operating system tools to change partition type, format etc
If you don't want to start over, DFSee,
dfsee.com might be able to save you by fixing the CHS values to how OS/2 likes them, shrinking a partition so have room for BootManager and IIRC, installing BootManager. Unluckily I don't think dfsee supports the BEOS file system so you would have to shrink the Windows partition and you still need a primary for BootManager.
Also a good idea to have a FAT32 partition for sharing data between the operating systems, FAT32 support has to be added to OS/2 after install, or use a FAT partition, which means for OS/2 8.3 name limits.
No you can't boot OS/2 from a CF card unless the hardware presents as an IDE drive.
BTW, Lenovo has (had?) a SNAP build for T42's, at least those with an ATI video display, also a sound driver. Don't know the URL as it has been a long time since I installed it to my T42. You can also use the Uniaud sound driver and the SNAP you have does work besides DPMS support.
Edit: feel free to ask more questions