Currently if both trays have letter paper in the trays, or have been configured for same type of paper there is no option to choose which tray to take from.
The only way to get the 500 sheet feeder to work or to be the Default tray with QuickDraw GX is to go into the Printing menu and configure the 250 sheet feeder for a paper size other than Letter, or different from the 500 sheet tray. Changing this allows you to use the 500 sheet feeder. However, once you change the paper size, the 250 sheet feeder will not be available.