I'm not sure how to use that formula...right now in a column that will
be hidden I have each cell marked =COUNTA(E1), =COUNTA(E2) etc. and
then at the end of each section there will be a sum of any cell that
has a 1 in it. this total would then prefill in another worksheet.

I've tried to play with your formula and can't make it work - what am
I doing wrong? I've changed it to =COUNTA(E1)-COUNTIF(E1,"N/A")