How to set CMT value for 2-compartment bacterial model

Dear NONMEM users, I want to set-up a bacterial model consisting of susceptible (S) and resting phases (R). I use Advan9 in NONMEM for the subroutine. With Advan9, one has to declare compartments. My experimental bacterial counts belong to both S and R (i.e. sum of S and R). And the compartments are such that: CA=(A(3)) ; compartment for drug DRUG=EMAX*(CA)/(EC50+(CA)) ; relationship for drug using an Emax model DADT(1)=K1*A(1)-(K2+DRUG)*A(1)-KSR*A(1) DADT(2)=KSR*A(1)-K2*A(2) DADT(3)=KDEG*A(3) A1=A(1) ; S A2=A(2) ; R ATOT=A1+A2 ; N=S+R A3=A(3) ; Drug Concentration IPRED = ATOT I'm wondering as to how or what to set-up for the compartment value CMT in the input file whenever I have bacterial count observations. I understand that the CMT for the initial drug concentration will be set to 3 since drug belongs to compartment 3. Thank you in advance for your help. Best regards, Sherwin Sy