How do I properly set/scale the calibration offsets values that will be the argument of the, for example, "accelgyro.setZAccelOffset( offset_value)" method?
I don't know, because I don't use that library. 0 might be appropriate for an offset, and 1 for the scale factor.
The magneto-corrected values for the accelerometer should be fed directly to whatever part of the code uses those measurements for the orientation calculations, which will assume that the appropriate corrections have been made.
In other words, skip the library-applied corrections, if you can figure out how to do that.