2 SCSI + 1 IDE= OK Then take away the IDE and no boot.

I'm running W2K server.  When we first installed it we put in 2 scsi hard drive in a raid 1 configuriation and 1 100 gig ide drive.  After a few weeks it became obvious that the 100 gig would be better sutied somewhere else.  I shut down the computer removed the ide hard drive and rebooted the computer.  I got a sytem failure message.  I freaked.  Eventually after trying several options I decided I needed to reformat the remaining hard drives.  I put in the W2K server cd and turned by back for a second.  The first message that comes up is "press any key to boot from cd".  I must have missed that because when I looked at the screen I saw the Windows startup screen.  So in conclusion if the W2K server cd is in the cd drive it boots normally.  If the disk is not in the cd drive the I get boot failure error.  Two questions.  First why does this happen and two how do I fix it so that I don't have to have the W2K server cd in the cd drive everytime I boot the server.