If they are PWM they might not need to run The fans should only come on if they are needed not spin all the time like they do in the MP. The fans in my computer are rarely on it has to under pretty intensive load to make them spin. There are many way to solve problems with PC's you just need to try a bit.
If you're board only has 2 fan headers you bought an inexpensive board and it's not really comparable to you MP.
Well I tested your theory and you're right. Fans only came on when temps creeped up. I moved them to the front. Only access to air is the sides of the front panel hope that helps. Thanks for all the help. I admit I have a lot to learn still.