I also have old tax liabilities that were paid online and somehow still showing up under "pay liabilities". I have tried putting a minus/negative amount in the expenses column to match the payroll liabilities that is flagged as overdue, as well as putting a zero in for the check amount, and unchecking the "to be printed", then making the check # say "EFT". It still won't take it because QB desktop wants an "account" associated with the negative expenses amount I am putting in. 
   What account should I use? One of my problem examples is using "local withholding" as the account the $$$ is supposed to come out of...