1) You would need to turn off the amp model and add the FX Loop and EQ. You would also need to be aware of how routing and the mixer were located in the patch. To be honest using stock patches from customtone may be tricky because I think the results may be difficult to predict and replicate.
2) No problem with leaving the POD in 4CM while using Amp models. It is effectively the same as plugging the POD into the FX Return which is probably the optimal amp setup.