Removing Windows 7 Old Partition?

I do an annual windows reinstall from an iso I made of the windows boot CD when I bought windows 7. I made the iso because it's easier to keep track of files rather than CDs, and whenever I would need to reinstall I would burn the iso to a disc, install from the disc, and throw out the disc once the install was complete. Well tonight I ran out of CDs with a large enough capacity to hold the iso, so I decided to get a bit fancy.

I mounted the iso and ran the setup utility through windows, and had it install a new partition of windows to one of my unused storage drives. The install went well, I restarted, and saw that there was an option to boot from two partitions of windows 7. I eventually figured out which one was the new one, and once desktop loaded up I went into msconfig and removed the old partition from the boot tab.

The problem pops up when I went back to reformat the old partition. It gave me an error stating that it cannot format a system drive. I figure that this is because the old partition is still active somehow even though I removed it from the msconfig boot menu.

Through a bit of googling I got a general idea of what had to be done, so I went into disk management and set the new partition to 'active'. I then restarted and went into BIOS, and switched the disk boot order so that the new partition came before the old partition. My bios did not like this, because it gave me an error about NTLDR missing. So it almost appears that the NTLDR thing isn't on the new partition, but that's just a guesstimation.

Other information:
- Old partition is "disk 0" in disk management
- New partition is "disk 1" in disk management
- I cannot modify or delete any of the system files on the old partition when I'm booted in the new partition.