You can't annualize for Federal if there are two schedule C's (or couldn't in prior years...).

MY solution was to (in a separate file) annualize and compute the penalty if any.  Then force the penalty in the file to be used for efiling.  IF/WHEN the government assessed a larger penalty, I'd print out the F 2210 & annualizing worksheets to use to answer the notice. 

All with the consent of the client so they weren't surprised when the nasty gram from the government arrived.

YMMV vis a vis Montana