Syncing iphone (3GS) with iTunes

[skb]

I always struggle to get books onto my old iphone (which I still use for reading). I usually use Stanza (and old version that actually still works) rather than iBooks.

Anyway, I wanted to put lots (100s) of books onto the iphone and I sync'd using iTunes (v10) via Calibre. Except now, when I go into iTunes, it tells me that it will remove all the books on the device to replace them with the new ones.

So, my question is, will it just replace any books I've imported into iBooks (ie none) or will it blow away my Stanza collection as well?

I'm frightened to try because I hate iTunes and don't trust it. Oh for Calibre Companion for the iphone (that's running old version of iOS so Stanza still works).