BOOTMGR is on a separate partition?

Hi Everyone,

I bought a new computer back in April '13 and i moved the HDD from my old computer into my new one. I created a new partition on that drive so windows could be installed and i named the other partition containing the old install and user data 'Old HDD'.
Recently i have had a few problems with external drives so i want to back my external drives up. I have tried to format the Old HDD partition but windows wouldnt let me because i assume it recognises that there is a windows install on that drive.

I read some posts about setting the partition as inactive so i set it to inactive and rebooted my machine for good measure only to find that when i did, the new windows installation wouldnt boot at all. This leads me to believe that my boot info is on the OldHDD partition which i have now set back to active meaning i can now boot into windows once again. I want to format that drive so is there any way i can move my boot information from the Old HDD (E:\) Drive onto my Local Disk (C:/) Drive?

Thanks in advance
Jack