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Install/running ubuntu on extarnal HDD with a windows laptop?

Ill take you through the steps I did. Sorry if this question has already been resolved, I'm new to Ubuntu and forums in general.

I have 2 internal HDDs in my computer, both with Win7. One HDD is my mothers, the other is mine. I did this because she didn't want my games on her computer, and my PCs motherboard took a crap on me, so I set up a dual boot.

I also have an external HDD. This is what I am trying to install Ubuntu 12.04 on. I formatted the drive by right clicking it, then selecting "Format". It is now in NTSF format. I downloaded the Windows installer, ran it, and selected "I:/" (my externl hdd) as the install location. The download and installation ran smoothly, and it gave me the reboot prompt. I selected "Reboot now" and my PC rebooted. I was then interrupted by the "Bootmgr is missing. Press CTRL + ALT + DEL TO REBOOT" message.

NOTE: I would like to use my HDD for a FULL Ubuntu installation, not the Live (i think thats what its called). I want all my files and settings from Ubuntu saved to the External drive as if it was my only drive.

If you need more information just ask. Any help would be appreciated. Thanks in advance.