between a HD and a CD-Rom DRIVE because I knew both drives were working fine but the CD drive wasn't working. Long story short, I fixed the computer even after it wouldn't boot several times. However, a part of the process confused me.

When I first changed the ribbon chords, it fixed the problem. Everything booted up fine. Then when I tried to restore from a CD, (and the restore cd was bad) it triggered more startup problems. The OS wouldn't load. After tons of problem solving tries, I switched back the ribbon chords and behold it worked. Very confusing SCENARIO. I also switched in and out of primary and secondary IDE controllers and tried booting from the HD and CD-rom several times. I never could get it to restore, but I got it working fine again.

Finally, does anyone have any idea as to why this would be? For my FUTURE reference?

(emachines, windows 2000 pro is all I remember about the machine)the reason I knew the CD drive was fine was because I switched in a brand new one and the same thing happened.One of the ribbon cables (that is what they are called in English) is faulty or damaged.
This also may involve jumpers as well but i agree with Contrex...
IDE1 = 2 drives.
One has to be set as master and hooked up to the END CONNECTOR of the ribbon cable.
The other needs to be jumpered as slave and hooked to the MIDDLE connector of the ribbon cable.
The same holds true for IDE 2 as well...

Also keep in mind that making more than one drive change at a time can confuse the BIOS and have it act as a cranky in-law.
Change only one drive/position at a time and always re-boot a few times to prevent this symptom...ok, but they worked fine going into both controllers with 2 different ribbon "cables". This is how they were set up in the first place.do you think that is what was screwing it up?Yep.