Split file in to two?

So I am trying to figure out if its possible with MCEBuddy but I would like to run a file through and remove ads via comskip (working right now).

Then I would like to run the file through to split the file in two.

I have searched for other alternatives and keep striking out really. I encode in h256 and I have files which contain 2 episodes that I need to split apart.

You could use the Custom Cuts application that comes with MCEBuddy to cut out the second half, process it and then use Custom Cuts again on the same source file to cut out the first half. This app creates an EDL to use during processing.