MegaZine3 supports chapters. Making use of this you can mix pages created "automatically" using the batchpages plugin and those you define manually.
You have to keep an eye on the number of pages in each chapter, since a chapter must start on an uneven page number (right page). If a chapter ends with an uneven number, an empty page (left page, even number page) will be inserted by MegaZine3 automatically.
How you can deal with that is shown in this little tutorial: