Since you are doing this via story board, all you need to do is insert the commercials you want, then click and drag them to appear between your video segments. If you don't have your videos uploaded as segments, you will need to re-do them so that they are in the segmented durations you need. For example, if you have a 30 minute show, but want a commercial break every 10 minutes, you will need to re-output your show in 10 minute increments and upload each one separately into Mogulus. Then it's just a matter of arranging your storyboard to play back in the sequence you want.
Hope this helps!