urknighterrant: You can either use a "door transition" tile, (there are several in each tileset, you'll just need to spend some time getting to know them), you can place a door and apply an area transition to it, or you can paint a type of trigger called an "area transition". You can also use a script attached to just about anything.
It sounds to me like you're trying to fly the toolset by the seat of your pants. I certainly understand the desire to do that, but you will learn a lot faster if you just put the skids on and follow a tutorial like this on all the way through...
http://www.noahwf.com/07spring/writing/AuroraToolsetTutorial-notes.pdf I like this tutorial because when you're done you have a nice little town all set up and ready for use in an adventure.
This is classic. It looks like the PDF is the same tutorial as the YouTube video I found in my search to answer the question.
