CTM and VM Workstation

Hi First post here.

I have a couple of questions.

First I have a Win 7 desktop. I have CTM installed and working on this desktop. I also have VM Workstation 7 installed on my desktop. Within VM workstation I have loaded a Win 7 pc contained within a separate drive partition on my hd.
What I am interested to know is if I load CTM on the Win 7 pc in VM will it mess up my current install on my Win 7 desktop in which the VM Workstation application resides. I am assuming not, since technically they are two separate MBR I just kind of want to check to make sure I do not hose my current desktop up. Which leads me to my next question.
When I loaded CTM I had just installed a fresh copy of Win 7 on a disk partition. On another disk partition I had another copy of Win 7 installed and on a different partition I had Win XP installed. I was using Easy BCD to boot between the various OS’. So I installed CTM on the fresh copy of Win 7 and protected the drive in which the fresh copy of Win 7 was installed as well as a System Reserved partition and a drive in which I had user data stored. I Did Not protect the partition which contained my old Win 7 or my XP. After CTM installed I was able to boot into my fresh copy of Win 7 and XP, but not my old copy of Win 7. Is it possible that CTM messed up my MBR? Hence my first question.

Thanks for any of your responses.

From what I have found I think this is a great product especially considering it is free, with a limited (no budget) I was surprised to find a product that worked like VM snapshots that I could use on my desktop and for free to boot. :-TU :-TU :-TU