Yeah, lots of stuff will "stain" them, such as colored drinks like gatorade. Its easy to clean though, just brush them with a tooth brush to clean time. You also have to wear them for 22+hours a day. Every set of trays is for 2 weeks, so every two weeks you are in pain for a few hours, unless you do what I did and change them before you go to bed and take some good painkillers. That way when you wake up, your mouth is sore, but it isn't that intense pain. Your teeth are sensitive for a few days though, but I imagine thats the same with metal braces.
Oh and I forgot, the smell of the trays is horrible unless you clean them every day.