If you mean that you don't want the AHRS program to assume that the MinIMU-9 board starts in a level orientation, you can make that change by editing this code (starting at line 224 of the file you posted, or line 171 of the original MinIMU9AHRS.ino):
for(int i=0;i<32;i++) // We take some readings...
for(int y=0; y<3; y++) // Cumulate values <-- Change "y<6" to "y<3"
AN_OFFSET[y] += AN[y];
for(int y=0; y<3; y++) // <-- Change "y<6" to "y<3"
AN_OFFSET[y] = AN_OFFSET[y]/32;
//AN_OFFSET-=GRAVITY*SENSOR_SIGN; <-- Comment out this line
(AN_OFFSET through AN_OFFSET are the accelerometer offsets. Normally, the program measures the accelerometer readings on startup, assuming the board is level, and uses those readings as offsets to zero the accelerometer.)
If you don't want to zero the gyro either (which you might not want to do if the board might already be rotating when the program starts), you can comment out the entire block of code in the snippet above.
Please let us know how this works for you.