You need to water at the base of the trunk. Also mist the leaves everyday. The tray is called a humidity tray and is just there to keep the air around the tree humid. I assume you were not told anything about bonsai when you bought this plant. A really good site for lots of info is www.bonsai4me.com
That site has alot of info about basics and really good descriptions about some more advanced procedures. Lots of very detailed info.
Hope this help you out. We both have a lot to learn about bonsai