Put the drives in the machine, one at a time, and be sure that they are jumpered as MASTER. Then, it will either boot, or not. If not, use Alt-F1 when you see the "boot blob" (it will be a black on white, text block, that says "OS/2", in the upper left corner of the screen). That will get you to a menu where you can restore saved configurations (if any were actually saved, and if they haven't been overwritten with bad ones - in that case use the original one). NOTE: that you may not be able to see the 'boot blob", if the screen blacks out while switching modes. In that case simply assume that it is there, immediately after pressing enter on the Boot Manager screen. You have about 1 second. If all goes well, that should get you back to where you started.
BTW, there are two basic INI files OS2.INI and OS2SYS.INI. The best way to edit them is to use REGEDIT/2 (REGEDIT2.EXE), IF that exists on the system (it came with later fixpacks for warp 4 I think), but you will need to be booted to OS/2 to use it. There are other INI editors available, but you will still need to be booted to OS/2 to use them. Look at HOBBES:
http://hobbes.nmsu.edu/ where you will find most things for OS/2.
Thoughts:
I suppose that you don't have the install media for OS/2. If you do, I would simply do a new install. It would be a LOT easier than trying to do what you describe.
Since OS/2 is installed on a "dos partition" (I assume you mean a FAT16 file system), I am inclined to believe that you have Warp 3, which is from the early '90s. That can still be useful, but not as useful as warp 4, from the mid '90s. If it is warp 3, you should update to fix pack 42. If it is warp 4, you should get fix pack 14 (I think that was the latest free one), plus some other things, but you still need to make it work first.
Being an experienced OS/2 user, I would suggest that I wouldn't even bother to attempt to change the drive letters, even though I have a pretty good idea of what is needed to do it. You, as a new user, probably haven't got any hope of doing it, simply because you don't have the experience of working with the system, and trying to help you in a forum like this, is very time consuming, and I, for one, just don't have the time to do it. If you can get one, or the other, of those systems to work, you will want to back it up, then play with it. If you decide that you like OS/2, I would suggest looking seriously at eComStation, and some newer hardware to run it, but do the research to find out what does, and doesn't work, before committing to something new. Remember, that Google will find lots of information, but you will probably have a lot of trouble trying to sort out the good information from the bad.
Have fun...