Once you sit down and order, they will give you a to go box to put it in. You just can't go to the podium (or call in) and order.
FYI: We have a few restaurants like that around here. We just go in, order, then immediately ask for a doggy box to put it in. One particular Mexican restaurant that I really like, I do this at all the time. The waiters know me and as soon as I order, want to know if I want a to go box.

I give them a hard time about not letting me order from the check in counter, but they just laugh and say that's their policy, but they have no trouble with me coming in, sitting down, ordering whatever, then getting a to go box to put it in. However, the kitchen is not allowed to put it in a to go box.

I tell them it just gives them dirty dishes to wash and an extra table to bus, but they still say it's their policy.