I figured out how to do this. It's not intuitive. The first step is one applies as much as the amount owed to next year's taxes (yes or no, no variations); then, when doing the estimateds, there is a step where it asks you how much you want to apply - it's a couple steps in, after the one where it looks like there's no choice. One (as in many Turbo Tax 'games') just has to keep answering the questions and keep moving along with "continue" and you'll eventually get there.
