The motor mixers are labeled A-B-C.... in the pictures, A=M1, B=M2, C=M3,.....
If you flip the board (IMU_FLIP = 1) than still be sure that the motor connections follow the mixer layout (if you not changed the parameter file)
For a X-Quad, GPS on top (IMU_FLIP = 1), following Clock Wise seen from above;
Board number 1 > M1 (A)
Board number 4 > M2 (B)
Board number 3 > M3 (C)
Board number 2 > M4 (D)
//Frank