How do I prevent my hydraulic brakes from getting pressed/damaged when the wheels are off?
Since bikes are usually shipped to the dealer with the wheels disassembled from the frame, the disc calipers often each have a plastic separator pressed into them that serve to prevent lock-up during shipping. The Hayes company even puts their brand logo on theirs. Since these are removed during assembly, you might be able to ask a repair person at your local shop if they have any extras lying around that you can just have to keep. 

EDIT: Here's a link to a how-to that gives the same advice, plus has some photos of the separator in use... http://www.singletracks.com/blog/mtb-repair/hydraulic-disc-brake-service/