System Commander can cause other problems if you should choose to re-install the operating system(s). Not saying it does all the time, but i have seen it happen. Setup will not allow you to continue a lot of times with a stop 0x0000007b error.
if you do want to install win95 onto E: and it replaces the mbr (which it will do), you can boot with the XP disk, choose recovery console and run these commands:
FixMBR
fixboot
bootcfg /restore
this should repair the MBR, redetect and reconfigure the boot.ini file to display the other OS's on the system. I would say wait till you have another HD if you are not familiar with the Recovery Console commands and switches.