Your dining reservations are not tied into your resort reservation at all. Your travel agent can make the seatings for you or you could do it yourself.
The one thing I would be nervous about using a travel agent to make my dining reservations would be what happens if the restaurant and the time you've chosen is not available? What would the travel agent then do? Make a decision on your part or have to call you back and update you. Then you would have to tell her an alternate plan, she'd call Disney back, etc.
You do it yourself and told something isn't available, you have your list of second, third, fourth, fifth, sixth choices right there.
I would just hate to have a travel agent try for a seating a restaurant that you've said you really want to eat at but the only time she could get was 9:30 and that's way too late for you. But she did what you wanted - she got you that reservation.