I had not received my EFTPS PIN yet, so I paid my 1st & 2nd quarter estimated taxes directly through IRS.Gov. How do I update Intuit Self Employed to reflect payment?

There are ways on how we can record the tax payment made outside QuickBooks, jb4250.

We can either record it through the Taxes tab or Transactions tab.

Here's how to do it in the Taxes tab:

1. Click the Taxes tab. 
2. Set the year. 
3. Select the Quarterly tab. 
4. Choose the quarter you want to mark the tax payment for.
5. Click Find your estimated tax payments beside Don't see your payment?. 
6. Check off the tax payment.
7. Hit Mark as tax payment.

If through the Transactions page, check your business spending transaction. Then, manually assign its category from Taxes & Licenses to Estimated Taxes.

On the other hand, I'd recommend reaching out to the IRS so they can check and verify why you haven't received your EFTPS PIN.

Once you already have your PIN and enrollment number, you're good to pay taxes online.

In case you have the Tax Bundle, you can make a payment on the EFTPS website or pay from your QuickBooks Self-Employed account. You'll have to do this on a web browser. I'll show you how:

1. Click the Taxes menu.
2. Select the Quarterly Taxes tab.
3. Select Pay Now.
4. Select the Online option.
5. Enter your EFTPS info and PIN.
6. Select the current amount or enter a specific amount.
7. Follow the on-screen steps to finish the payment.

Afterward, QuickBooks sends the payment to the EFTPS immediately after you submit it. It can take 5-7 days for your payment to show up in your payment history on the EFTPS website.

There you have it, jb4250. Feel free to tag my name if there's anything that I can help. Have a great day ahead!