From what I understand, you call Mears the day before you want to head to US/IoA. Tell them about what time you want to leave, they will give you a pickup time. You pay when you get on the bus, I believe. Then, you can either prearrange a pickup time to return to WDW or you can call Mears 2-3 hrs before you're ready to leave and they will tell you what time they will be there.
I just booked a special, that is offered by DU, where I paid $118 pp for Mears shuttle service and 'two parks/one day' at US/IoA. It's all prepaid which is nice. If you buy passes directly from US, you pay that just for your park pass. Booking as I did got me my ride free.
And they pick you up right at your resort.