I filed an extension for 2016 tax year & paid $500 towards my Federal Return. I'm trying to finish filing & pay the remainder but I dont see the $500 deducted frm total

Hi I started my 2016 tax return in April and filed and extension.  When I filed the extension, I paid $500 through Turbo Tax to apply towards my Federal Return.  I have returned to finish filing my return but do not see the $500 being deducted from the total I owe.  When does it show?  I was at the point in the return where I had to pay the fees to file the return.