I'm sorry, I don't really know what the solution is. I just know that in my experience, Samsung's contact manager is pretty awful, and I wouldn't let it manage my GMail contacts by telling it to merge anything.

Theoretically, it should automatically merge the contacts on the phone side. It should be smart enough to know that if you have a Joe Schmoe as a Facebook friend, that's most likely Joe Schmoe from your GMail contacts. That's how it works in stock Android in ICS and above with the People app. I didn't have to do anything, but the app knows that my wife is the same person in my contacts, Facebook, and Twitter.

I would also recommend that before messing around with your contacts in any way shape or form, you should always go to GMail and make a backup of them. Then at least if you mess something up, you can always go into your phone and turn off all those social networks, restore your contacts in GMail, then bring them back down to the phone.

Sorry I couldn't be more helpful...