For the past 2 weeks, I have been experimenting with different fan configurations trying to keep my computer cool. My case has mounts for 4 fans in the front, 1 60mm in the back, and 1 on the side over the CPU & MB.
In every configuration, I've found setting the side fan for intake is the best. Now, I have no idea what kind of case you have, but I would highly recommend one with 4 front fans, a side fan, and if possible 2 back fans.
Besides setting the side to intake, putting the 4 front fans for exuast is best I've found too. The only problem I've found with that config is it makes the back the intake. And when most, if not all, power supplies are exuast, it just recycles the heat. Out the Power supply, and then back in the rear. Something you could do to solve that is to put a deflector over the power supply exaust. (attached picture on next post) Since heat rises, once you start it up, it should keep it going.
My overall rule of thumb is: The more exuast fans you have, the cooler your computer will run.
As for doubleing the CPU fan speed, I don't think that will help. It's morelikly the problem is the heat isn't leaving the computer, and your CPU fan is just recycling the heat. (plus I've never seen or heard of one that runs 12000 RPMS)
P.S. If your CPU fan is 6000 RPMs, you probably have a pretty good one. I recently purchased a Thermal Take 1500 to 6000 RPM fan&heatsink, and It's been great. Oh, and if your interested in a new computer case, check out Gigdot on eBay. I got my for under $40, S&H included.