BOOTMGR is missing issue, sorry.

So I recently did a fresh install of Windows 7 Ultimate 64-bit on a new HDD. Everything worked out fine and I was able to transfer over my documents and such perfectly over from my old HDD (with W7 Home 32-bit) to my new HDD (with W7 Ult 64-bit). I was tired of having to choose a which HDD to boot from every time I started my computer so I tried to just format my old HDD since I've already taken everything I needed off of it.

Disk Management wouldn't let me format it so I tried to change the label from C: to A: seeing if that would change anything; then changing my new HDD from E: to C:. It wouldn't let me do that so I restarted my computer and BOOTMGR is missing pops up. I go into my BIOS and figured I had to boot from my old HDD to get an option to load my new HDD's OS. After looking closer I think the problem is that my old HDD has the "System" property on it while my new HDD doesn't.

I guess my question is: what's the proper way to format an old HDD so I can only boot from a new HDD with a fresh installation?

TL;DR: Installed new OS on new HDD. Want to boot from only new HDD, format old HDD and use it for storage only. How to do properly?

NOTE: Please consider that I would not like to do another fresh installation as I've already downloaded and installed programs and such. I'm on a really low speed internet connection so I would like to avoid that at any costs.
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More about bootmgr missing issue sorry
  1. when installing windows its best to disconnect all drives except the one you are installing to

    this saves the other drives being on the mbr

    try this to repair the boot record
  2. Thanks for the reply. I'll try that.
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