Looper pedals can only loop anything going into its input. So in order to be able to lay clean, wet, or dirty tracks over another you will Have to have all those switching options before the looper. 

So it would have to go guitar to pre amp effects chain (the prefx on the code amp after any pedals in your chain) then the pre amp model, then the modulation, delay and reverb, then the effects loopb then the power amp section, then cab simulation (if on). 

So if the pedal is last in the effects loop it will have every chinge in any preset minus the power amp section and the cabinet simulation. As far as my underatanding goes about the amp. Thats how i do it anyway and it captures alot.