Ooh, that's a really interesting concept / question! The bad news is the way Zine Arranger handles lots of pages is gonna make this especially tricky.
Right now whenever there's more than 1 sheet worth of pages, Zine Arranger sets things up so that each sheet nests into the middle of the previous -- so like for a minizine, you'd open the first sheet to the middle, lay the 2nd sheet in there and so on, and then staple the spine. But for gluing the 2nd sheet to the 1st sheet, you'd need a totally different page order...
It's a bit of a pain, but right now my best suggestion would be to separate each sheet into it's own 8-page PDF -- then you just have to make the first and/or last page blank, depending on where the sheet falls in the order.
It's good to know about this method of making a longer booklet, though! I'm glad you reached out. I added a note about it on my to-do list. Someday when I get a chance to add some features to this, I'll try to add in an option to have the pages arranged in a way that would work better for this--maybe where each 8 pages becomes 1 complete minizine, in order instead of expecting to be nested into each other.