If this is a non-compact frame, then the height of the top tube controls the height of the head-tube. If you want to get your bars very low, then the smaller frame size is better. If you want the bars higher, the the larger size.
If the top tube is 1" lower, and you have an extra inch of exposed seatpost, it really doesnt make any difference to the saddle position.

How do the frames differ in top tube length. This is the really critical dimension, that will affect your reach to the bars, and the stem length you need.