Hi Tori,
The way engagement programs work is that they check before each send to see which content leads have not received, and then send them the email highest in the list that they have not received. Once leads have exhausted all content, if a new email is put into the stream, regardless of location, they will receive that one next.
So to answer your question - you can place the email anywhere you want in the stream and the other emails will not be affected. The only thing that will change is the order people receive the new email versus the existing ones.