As a contractor (they have a 1099 form on file for me, along with a signed contract), I send them a monthly invoice using the invoice creation system they have implemented. It's not the slickest user interface, but it works, allowing me to enter my daily hours -- to the minute -- as required by the agreement.
Their payment terms are net 30; I wonder how long it will take for the check to get here? They don't do direct deposit. I can live with that.