Can I temporarily disable shortcuts when a certain program is running?

I'm using Inqscribe, a transcription program, and I want to assign certain shortcuts, like ⌘S and ⌘F, that are already assigned to certain functions with my Mac.

Is there a simple way I can disable all shortcuts when using this program, so I can assign any shortcuts I want in this program? If so, can I have it set up so it disables shortcuts automatically when I open my program?

I'm using Os X 10.6.6.