Do them in between, I would. I should think it would be obvious when the story is continuing, and if not you could always get one of the characters to do a little recap in a speech bubble and make it part of the comic.

You could always draw the other comics when you get the ideas, but post them once the story arc is finished?

Those who have been paying attention to the story arc will be able to easily see the difference between the continuing story arc and the little comic ideas.