Most states, and the feds, have a website where taxes liabilities are entered and you authorize the payee to electronically take the funds from your cash account at the bank. In DBA payroll, after you have properly setup payroll defaults, you will run payroll, which will keep track of the tax liabilities, and then you will transfer those liabilities to Accounts Payable. Once those amounts are in accounts payable, you will select the vouchers to pay to the tax entity, and issue the check. We print the check to plain paper, and authorize the tax entity to do the electronic funds transfer using their website.
 
Steve