Something is screwed up in your setup. It should be syncing, not replacing your content. I looked a little last night and didn't see an obvious answer. I will try looking again tonight.
Are you on a Mac or a PC?
Well we have 2 iphones with 2 different names. We both had iPod Touch(s) before so when we sync'd our new iPhones I think something got messed up. Anywhoo....We're using my MacBook.
Besides that little blip I think all is fine now since we have elected to manually backup which is safest anyway because it's a full backup right? Unfortunately no way to visually verify a backup.
I just transferred all the apps I purchased on my iPhone to iTunes so now they DO show up in the apps tab on the iTunes left sidebar just like music shows up in the left iTunes sidebar music library AND they show up in the iTunes iPhone app tab up top too.
So now if I want to send my iPhone iCal, Mail, and Address Book data to iTunes/MacBook do I just go to the iTunes iPhone info tab where it says Contacts, iCal, Mail etc and sync? Obviously right...but how do I make sure that my iPhone data overwrites the MacBook data and not the other way around?
Btw, someone else told me on this forum that I should create a separate MacBook login account so that all my stuff stays separate from my wife's. I think that's overkill no?
EDIT: Other quirk... iTunes really wants to over ride everything on my iPhone. eg. I move things around on my iPhone but when I sync or transfer purchased apps to iTunes, the order of apps/pages etc in iTunes takes priority and my iPhone inherits the setup that was in iTunes. Big Mo' Fn' circle I keep goin' in lol