No, you want to point the fan DOWN into the heatsink so that it blows air across the heatsink. The rest of the air pressure from the chassis fans will do the work to evacuate the warm air. There is a standard fan header (actually, I think there is two) that you can utilize off of the motherboard. Obviously, with a smaller 40x40mm fan, there is no chance it will draw too much voltage/current to damage the motherboard (unless it fails in some spectacular way).
Now if you've removed the upper sled, and both are on the bottom, then yes, I'd personally replace the front fans with quieter 80mm fans, and then install one or better yet two 120mm fans near the rear that SUCK air out, this will improve the cross airflow across the cpu's, and yet keep the noise down. Now, if there is enough room, you may even get away with mounting a traditional HSF to each cpu. I don't know if the motherboards can support mounting a standard HSF though, so that might be more custom work then its worth... unless you go liquid cooling, but now your talking $$$, and you might as well sell the whole darn thing and buy a newer gen C6100 that runs cooler and quieter stock.