Yeah you need the application for the ext .bootskin to work 
same as you need word for .doc or a browser for .htm or a mediaplayer for .avi... etc. etc.
You can also modify your windows installation manually this is what bootskin does for you so you dont have to "hack" your windows copy, mind you that hacking it manually is a bit dangerous (might happen that windows wont boot) if you dont know what you are doing thats why bootskin was created 
I have done it manually before, bootskin is a improvement hehe