Boot Manager does support being on disk 2. However, for some reason the LVM program from IBM doesn't provide a way of putting it there, even though the LVM engine (API) itself does.
You could try my incomplete LVMGUI replacement... It's only half-finished, but I
think installing Boot Manager is one of the things I actually implemented. (It's been a few years so I don't remember clearly.)
http://www.altsan.org/os2/toolkits/lvm/lvmpm_bin.zipThe idea is that you select the second disk in the bottom panel, then choose System->Boot Manager->Install.
No promises that it will work, but if you have no other options you can try it.