Hey fabsn,
I'm pretty new to Megazine so I can't really walk you through it. But yes, you can run multiple flip books from one installation, and there's an excellent walk-through which you can find by going back to the main forum page, and looking at the top links (highlighted pinkish-orange) under Version 2, General Discussion. I think there's also a video tutorial on YouTube that covers this material.
Good luck.