In order to pay the MLS dues for a Team ID, you have to be logged into Matrix under the Team account. Use the switch in the upper right of Matrix to log in under your Team ID:
Once logged in as the Team, go to the External Links widget on the Matrix home page and click on Membership Center & Dashboard:
That will bring you into the Member Dashboard- you should see your Team ID name in the upper left.
Just click the Pay Now button in the upper right and go through the steps of paying the bill.
Once you are finished your Team ID will be paid.