This was a major pet peeve of mine.....
While working as a bartender at a restaurant, we were supposed to take carry out orders.  Fine, no big deal.  But, the carry out sales were added to our total sales, which meant that we (as the bartender) got taxed on in-restaurant sales as well as carry out sales.  So, in answer to your question, you should be tipping the carry out person in a restaurant.  Other carry out places (like sub shops or whatever) don't follow traditional restaurant rules.  Well, I think that you should anyway.