Did you enter it in the dialog in the image below?  See the highlighted area, Other Payments.  If you don't use the Remittance Feature of the program, you need to enter it in this box.

Yes I enter it manually, but I want it set up to be automatically entered. Is that not possible? Do i not have something linked or set up properly?

As I said, if you don't use the Remittance feature in the program, you must enter it manually.  You seem to have entered it manually therefore, you must not be using the Remittance feature.

I don't use it myself but you can set it up under Setup, Settings, Payroll, Remittance by selecting the proper vendor for the tax/deduction you wish to use the Remittance feature with.

Then on the Payroll module home screen, you can select Pay Remittance.  This will automatically open the Payments module and change the transaction from Pay Invoices to Pay Remittance.  I tried to upload an image of this but it will not upload properly for some reason.

I believe the sample file has it set up so you can see how it operates and you can try it on a copy of your file before you set it up on your live file.