Hi, QP values can be specified by 'QPISlice' in 'encoder.cfg' file under 'bin' folder, or you can directly specify the 'delta_quant' in the source code.
The software modifies FMO type 2 so as to be able to encode the defined slices in different quality (i.e. different QP for each slice). There is an example in JM/bin/example and a README file therein that explains how to do it. Try running that example and reading the referenced paper. Hope this helps.