iBooks sync question iPhone

I just put the iBook app on my phone and have several books in my iTunes I would like to sync up. When I clink sync I am told that syncing iBooks will remove any other books from my phone. I am fairly certain this only applies to books in the iTunes library, but since I have about 600 books on the Stanza app, I am worried that syncing the iBooks will somehow mess with Stanza.
So, can someone reassure me that Stanza will remain as it is if I use the sync option on my iTunes for the books?
iOS 4