If you processed the payment through Tasks - Record Manual / Print Quick Checks and chose the EFT option, it sounds like the invoice could have been created again.  So, if it has been entered twice and only paid once you'd see what you've described.  If so, you would void the open invoice using Tasks - Change Invoices. 

What went wrong?  If the invoice was originally entered through Tasks - Enter Invoices, then when it was paid through Record Manual checks, when the cursor is in the Invoice # box, someone should have clicked the List button and selected it from the list of invoices already entered.  Instead, they may have entered it again, and just slightly change the invoice number (therefore, it would not be recognized as a duplicate) and so created a duplicate invoice that is paid by the manual check (EFT), leaving the original invoice unpaid and open on various payable reports. 

When I do an ACH payment, do I do the same thing as I do when printing a check except I'll take the Electronic option instead of the Check option?

An ACH payment is different from EFT payment.  If you need to send a transmittal to the bank to pay the invoice that meets NACHA requirements, it is an ACH method.  

If you are just doing an online payment, say for taxes, you would use an EFT payment method.  

ACH works like this:  https://us-kb.sage.com/portal/app/portlets/results/viewsolution.jsp?solutionid=232425080900047&hypermediatext=null (save the file it downloads and follow the directions.

EFT works like this:  https://us-kb.sage.com/portal/app/portlets/results/viewsolution.jsp?solutionid=223924350032580&page=1&position=7&q=EFT%20PAYMENT 

I have the same question.  The ACH pdf you reference is exactly what we have done as well.  However, it is keeping electronic payments (not EFTs) on the AP Aging.  Why?  How does that change?

There are a number of possible reasons.  See:  https://us-kb.sage.com/portal/app/portlets/results/viewsolution.jsp?solutionid=223924850045693&page=7&position=4&q=ach%20payments%20still%20show%20open  

Most of these explain either something was left in the discount, the retainage, or the distribution.