In general: There's no simple way. But I'll outline an approach.
If you don't care about changes being overwritten: Keep a timestamp of the most recent change to each record, and a timestamp of each sync. When syncing, you get a list of all updates on the iPhone since the last sync, and all updates on the server. You write from the iPhone to the server if the iPhone timestamp for that record is newer than the server one, and vice versa.
But you probably care. Say you've edited a note called "Where to meet up on Friday." It started out empty. Now, on the phone, you've written, "My house." Ten minutes later, your friend edits the same note on the server and writes, "The diner." Who wins out? Stack Overflow can't answer that for you; it's application-specific.
OK, so modify the approach above: if both the server version of a record and the local version have been edited since the last sync, then you have to ask the user what to do. That's the basic algorithm.
If you care a lot about changes not being overwritten, to the point that you want to merge changes to different places in the same documents, then your system will begin to approach the complexity of version control systems like Subversion or Git. Not at all simple.