You could try setting up an override comskip.ini and experiment with the parameter
thread_count=1
;Number of threads used when decoding the video
;;Increasing the thread count speeds up the processing on CPU's with more cores then the current thread count. Setting the number to higher then the amount of cores makes processing slower. Setting the thread_count to 1 disables multi-threaded decoding, useful in case comskip crashes when decoding the video.
I'm guessing if you set it to 4 it will use 50% CPU, 6 would use 75%, etc.