Dual boot problem

I have a PC that has an ASUS P4B533 board, a 1.4 Gig Pentium4 processor, a 40 Gig hard drive, and 256 RAM system. I have configured it to run both Windows XP and Windows Server 2003, standard edition.

I installed Windows Server 2003 last so that it is using the Server?s boot manager. The problem is that whenever I boot from a Windows 9X diskette, I ruin the boot manager (I get the message stating that there is no fixed disk installed or something to that effect). And then I cannot repair either OS. So I have to install the Windows Server 2003 again to get the system to dual boot. Can anybody please help me out? THANKS.