Estimated Tax Payments

I estimated tax payments of $750 per quarter.  However, I worked my side gig more than expected and my estimation was way off.  I owe a little over $5,000.  I have several questions related to this:

--I paid estimated taxes of $3,250, but in my IRS account shows only my direct payments of $1,750. (I have documentation of all the payments).  

 

Question 1: Will I get an audit if the taxes I paid does not match what the IRS shows in my account? (My other payments went thru another payment system offered on the website.)

Question 2: I am ready to file and pay my taxes through Turbo Tax. Should I just pay what is owed through my direct IRS account?