The problem is the out put is not matched between your clean and dirty channels.

Three solutions:

1) record the clean and dirty tracks on different channels i.e. separately

2) balance the output of the clean and dirty channel

3) record the whole lot as a clean channel and add distortion later with a plugin.

Expect to have to adjust input level with every different input signal !
Unfortunately this is one of those "whatever it takes to get a good recording" moments.