It very easy to replace bookmarks stored your computer in safari or internet explorer to your iPhone but this way iTunes will delete all the bookmarks stored in the safari browser on your iPhone and overwrite with all the bookmarks on your phone.
But what if you want to backup all your safari bookmarks so that you can restore them on your iPhone by syncing next time after firmware upgrade. It was some what different case with me, as I want to backup all the safari bookmarks on my iPhone so that I can restore them back after jail breaking my iPhone 3g.
Lets see how can you backup all your iPhone safari bookmarks on your computer browser including Safari or Internet Explorer
1. Connect your iPhone with data cable and run iTunes
2. Now, select your iPhone and click the Info tab, select Sync Bookmarks With Safari or Internet Explorer
3. Make sure that Bookmarks should be unchecked under Advanced
4. Click Apply button after setting all these options, and it will start syncing your iPhone safari bookmarks
5. After some time it will ask you to allow changes due to some of the bookmarks copied from iPhone Safari Browser, click allow to let it proceed and copy the iPhone safari bookmarks to your computer browser.
That’s it, After sync is complete you will see your iPhone safari bookmarks in the respective browsers you choose.