Not familiar with how Linux works, but you can read up on OSL2000 which says it supports Linux as well. click here
I have tried OSL2000 on a setup involving 2 hdds, multiple partitions, but all were Windows OS's. Worked fine.
As far as I'm aware, any boot manager will write itself to the MBR, in order for it to "intercept" the normal booting and give you the choices. I'm sure you're aware of that. OSL2000 works in the same way.
OSL2000 always installs itself to the MBR of the primary master, so if you're using the XP hdd as the primary master, to that limited extent the MBR on the XP hdd will be changed (but it's nothing drastic). During the installation of OSL2000, you get a chance to back up the MBR on to a floppy, which can be restored. (In any event, the original MBR can be rewritten by using a 98 floppy or XP Recovery Console).