ADVAN5/9 ISSUES - PDxPop4-NONMEM Users

Dear All, I am using PDxPop4-NONMEM. When I am using ADVAN 5/9 in my control file I come across this sentence after $PK line (S1=1 ;modify as req'd for scale parameter &/or dose-obs unit differences). I didnt understand this. I went through the PDxPOP 4 Manual (Page #107/108 ) which is written as follows. The control file is complete with one exception. The correct compartment for scaling the observation, S2 in this case, was selected but the parameter for scaling, for example V, cannot be known apriori and must be added by typing it on the S2 line (e.g. S2=V ;). Also, any correction for differences in units between the dose and the observation (e.g. AMT in mg and DV in ug/L) must also be added manually to the control stream (S2=V/1000). Make any required changes to the control file, save, and close the file. The new file will now be found under “Control Streams Selected” on the Model/Run Tab and the model can be run. I didnt get their point yet. My model isnt working if I ignore this sentence and I think it could be probably because of the above reason. I appreciate your suggestions. Thank you very much.