I use Sage BusinessWorks 2021 and this is how I would pay an EFT that payment has already been made to the vendor (online).  If the invoices are all to one vendor, you can go to A/P, hoover over Checks and click on Enter Payments in drop-down menu.  Once in Enter Payments, select vendor id, this brings up a list of invoices due to that vendor.  Click on Circle by EFT #, you can then select any number that would help you find this payment in the future.  Enter the total amount you want to pay, select the invoices that you want to pay and make sure the undistributed amount is $0.  Click on Post Only, then it should bring up a message do you want to print.  

Correct.  You would use AP, Checks, Enter Payments.  Sent the vendor.  For Type, indicate EFT.  Then enter the amount and on the bottom select the invoices and amounts to post to those invoices.

Are you working with your bank on this as well.  Doing this for another client right now. Coleen is correct for after the fact but for doing before and sending a group is a bit different.  I can help with more clarity