Just so I understand this, you want to use Custom Cuts to manually mark commercials to cut out and then also use Comskip to automatically detect commercials in the same run?
In a single conversion you can either do Custom Cuts or have Comskip detect commercials.
If you want to do both on the same video, you can setup a daisy chained conversion, where first you do a Custom Cuts and then you run the converted file through a second conversion to have it automatically detect any commercials. If you’re using this it’s best to use an Unprocessed profile on one of both conversion tasks to avoid loss of video quality.
You can find more information about daisy chaining here: