Xathro knows way more than I do, but I will throw in my neophyte experience with the I/O Linc. You want the Relay to operate in one if the three (A or B or Momentary modes; you also want to set the duration of the On state to be long enough for the door to close, e.g. 10 seconds.
You set this in Admin Console, click the relay and choose the Options button.
Activating the relay (turning it on) has the same effect as pressing the garage opener wall button; you complete the circuit and the opener activates. Putting the relay in one of the three Momentary mode (A, B or C) will turn it off after the elapsed time.
I have my ISY setup to text me if/when the garage door remains open for more than 5 minutes and then again when it closes. Every 15 minutes between sunset and sunrise, another program checks the sensor and if the door is open, it activates the relay to close it.