I failed to file on time. I am ready to file today and have the funds to pay what is owed. Do I just file and pay? I don't know what to do

Yes just file and pay as normal.  You can efile until Oct 15.  The IRS will send you a bill for any interest or penalties.  You can pay right away at https://www.irs.gov/payments 

FYI ... hopefully you filed an extension ... if you did not then  expect a bill for failure to file timely  along with the failure to pay timely + interest.