My HSA is not Pre-taxed, how do I file for deductions?

Hopefully I am explaining this right. My workplace provides us Healthinsurance for an HSA account, however no money is deducted from my paycheck for the HSA as "pre taxed",. What we have to do is, open an HSA account with our personal bank (I did this through my local Credit union) Then I take the "after tax" money from my check that gets deposited into my checking account and manually deposit $ into the HSA as needed to pay my medical bills. My employer does not contribute any $ to the HSA at all. There is no HSA deduction out of my check at all. 

 

I had a ton of medical bills this year. For about half the year I put $$ into the HSA from my checking account(after tax $) to pay these bills. This $$ was not pre taxed $$$.  The 1st half of the year, I was just paying the bills directly out of my checking account because I did not have the HSA bank account setup as I never needed it prior to this year.

 

Where and how do I deduct this using the webbased tax filing, especially if some of the bills were paid straight from my checking prior to having the HSA account setup to pay from?