What you are allowed to deduct is 50% of your actual meal expense or 50% of the M&IE rate.
Since the deduction limit for local business meals (entertaining clients and so on) is also 50%, it doesn't actually matter to your final tax where you report it. I assume that in the travel expense section, Turbotax asks separately about transportation, lodging, food and other incidentals, so I would enter it there.
I believe that Turbotax wants you to enter the entire expense and Turbotax will perform the 50% calculation. However, another expert should confirm this for me, or you can check yourself by verifying your schedule C before you file. (I don't have the actual program handy on my current computer.)
