So I noticed there was only one set of accelerometer and gyro data in ardupilot, so I added suppprt to my github checkout this commit
the majority of the code was already there. I also turned off the low speed spi function on the lsm9ds1 magnetometer. This allows you to start ardupilot with multiple ekf cores realistically this only gives us redundancy as ardupilot does not use both sets of imu data it only uses one and the other as a backup as I understand.