Hello there David,
In short, as it stands right now our plugin only works exclusively with InDesign. We do have a free tool that will quickly convert a properly sized PDF file (with multiple pages) for the iPad to a .mib file (Mag+'s proprietary file type). However you would not be able to add features & enhanced functionality going this route. If you simply want to start with PDF replicas though, this would be the way to go:
Otherwise we recommend utilizing InDesign to get to most out of our powerful tools!
Please let me know if you have any follow-up questions & I'd be happy to answer them!
Mag+ Support Team