I don't think there is or will be a good fix for this.  I've been taking the approach to evenly divide all estimates paid by Nov 16 by three and manually inputting them as paid on time in the Q1, Q2 & Q3 inputs.  I realize CA estimates aren't due on that schedule, but I'm checking to make sure no penalty is generating and moving on.  It's not perfect, but that's how I'm handling it as of now.