Installing an application in a Bootcamp partition under VMFusion 5

I am running Fusion 5 on a MacBook Pro with MacOS 10.7.5.

I have Win 7 installed on a Bootcamp partition and was wondering if I install an application while running this OS inside VMFusion will the application be available and run correctly when I next boot directly in to the Win 7 partition (from start-up NOT VMFusion)? Or am I best just boot directly and install from there?

Thanks in advance.

Steve