Nightmares Alternating Between 2 Bootup HDDs?

so ever since I got Windows 7, i have had nothing but nightmares alternating between 2 hard drives.

before back when I was running XP I had 2 HDDs that I would alternate between. both had XP installed, one of which was for backup. whenever I had a problem with my current OS, I would just swap the HDDs and run my backup while I image the other screwed up one.

now with Windows 7, i cannot do that because of the STUPID bootloader. bootloader made me have nightmares at night. pretty much what happens when I swap it says "BOOTMGR is Missing". now whats really messed up is that, I think the PC stores the bootloader info NOT ON THE HDD, but somewhere in the BIOS or mobo. because i completely disable the old HDD that I used to bootup with 3 partitions, and the one im trying to boot up has 2 partitions and it worked perfectly. but since i used norton ghost and try to boot up after restoring a backup of 7 on it, it says "BOOTMGR is missing".

both of my HDD windows got screwed up, and even my CD ROM STOPPED WORKING! i couldnt even recover it from the W7 disk. but I maanged to fool the system by swapping CDs and finally got into the recovery and repaired one of my HDDs boot loader. but the one I need it to work within 2 days is still messed up. can someone explain to me how this bootloader works and what i need to do?

I got 7, XP, and Vista on SATA, and 7 and Ubuntu on IDE. both worked fine whenever I needed to swap between them until i messed with Norton Ghost

do i need to format my HDD and write 0s to it? it worked for my SATA that wouldnt boot up and give me NTLDR error before. same crap with W7 bootloader.