Once you've wrote your payroll checks, you will have accumulated payroll taxes that need to be paid off. This happens automatically if you import your payroll from Paychex, but if you don't use Paychex, you'll need to account for it manually, and this article walks through how to do that.
The type of transaction you'll need to make will be either a check or a payment, depending what method you're using to pay the agency who is handling the taxes. If you are sending the agency a check, you'll want to create a check by clicking the "New Transaction" button and then choosing "Check". If you are paying them electronically or online, instead of choosing "Check", choose "Payment".
After setting your payee, date, and memo (Also, a check number, if you're writing a check), on the left side of the transaction, select the asset account(s) you'll be paying these taxes out of (You can also use a restricted fund, if you're going to be paying the taxes out of a restricted fund). For the amount, fill in the total amount you'll be paying this agency.
On the right side of the transaction, select the liability account that has the payroll taxes you're going to be paying to this agency, and fill in the amount that you're going to be paying. Both sides of your transaction should equal the same amount. When this has been filled out, you can save your transaction.