Quad Copter does not respond correctly after installing Arduino

When I received my quad copter it flew fine but in reading many blogs and watching many videos it was obvious Arduino was the best config for quad copters. I have a ATmega2560 CPU, MPU6050 Gyro and Accelerometer, HMC5883 MAG, and MS5611 Barometer board. I followed the directions on how to upload but now I can not arm the helicopter with the left stick (it arms with the right stick pushing to the right) and to disarm I have to hit the yaw trim button 3 times to the left and then push the left stick to the bottom left. Also when it does arm the motors are spinning around 3000 rpm even though multiwii config says idle is 1200 rpm. Not sure what the problem here is but the quad is now unflyable. Any help would be appreciated. I have searched all the forums and tried about 50 different suggestions without success. This board is on an Aerosky C6. Attached is a picture of my board.