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Not sure why you're having a problem, should sync automatically through iCloud connection...unless you don't have iCloud enabled.

You could try going to iTunes and when your phone shows up under Devices do a Sync.
 
Hmm I have phone set to sync vs iCloud. Have IOS 6 on my phone and mountain lion on my macbook pro. Still cant seem to get the bookmarks to sync up.
 
You would also need to check off in iTunes synce bookmarks. If I remember you need to scroll down in the contacts calendar tab? It's right by sync notes...
 
Thanks guys, found the problem. For some reason in icloud settings on my mac, safari sync was turned off.
 
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