To answer your question, I'd recommend placing the stove as close to the existing furnace as possible.
But, I'm not convinced that connecting a Keystoker 90 to your entire HVAC cold air return is the best way to go. Unless you have a very small duct system, I don't think the 90 would put out enough heat through the 6 or 8" hole on top to provide a significant amount of hot air to your main HVAC return. Furthermore, would not the HVAC fan, if you use it, also strip too much heat off the stove, thus cooling it too much? I estimated that I could probably service 2, maybe 3 registers with warm air from the Keystoker 90, and use a separate closed loop return (from the existing returns, or just create a new, smaller one). Anyone with a 09 have experience with all this?