Remaping keyboard keys

[Telperien]

Hi, i`m in the process of rebuilding my UI and I was looking for something to remap few keys on my keyboard, like windows key etc. I`ve found SharpKeys that works in windows remaping my Window Key but doesnt work ingame. More searching and I found autohotkey that can do it. There is my concern, would it be allowed to use AHK for remaping my keys? Maybe you know how to swap Windows Key to Control Key?

I use Windows 7, keyboard Logitech k400 plus.
Appreciate any help and clarification from GMs.