I recently came across an excellent post from someone struggling with that same question. I hope it helps you: http://blog.cloudfour.com/responsive-design-for-apps-part-1/

Although I am currently writing a book later out this year, my "day job" is running a creative agency where we've created several responsive websites, including http://newportdunes.com and http://searchoptimizers.com I find that sketching it out first allows for the constraints of the design to focus on what is most important. My favorite tool for this is UI Stencils responsive sketch pad, found here: http://www.uistencils.com/products/responsive-sketch-pad

I know you are specifically asking about an app and not a website, but I think it can still be a useful tool in the "fingers first" thought process and decision process. In Jason's post, he recommends Appcooker.com as a ipad based tool.

I think you'll find that Mobile or fingers first is a fantastic mindset with little downside as it forces you to get clear on the context of your content, size targets appropriately, and then the desktop design does not suffer for it. We sometimes go the other way, too, but we understand what "fluff" we give up when moving to the mobile side. Google Luke Wroblewski for more excellent info on his Mobile First way of thinking.

Good luck and let us know when your prototype is up!