Even if you prebook/prepay, you still just get on whatever bus you want to, on your way there. When you're going through the process online it LOOKS like you're saving a spot but you aren't...
I don't know if they take CCs on the bus. We paid cash, while on the bus, for the roundtrip, and got the nice r'trip discount! (full disclosure, we were on the bus from/to LAX, but it's the same)