Well I've only worked with RPG XP for a short while now so I can only tell you what I understand about the different layers. First there are three layers of graphic design and one layer of events. The graphics from each layer from the bottom to the top stack upon one anothers. If you try to place an object upon the floor or another object without moving up a layer then you will get some nasty whitespace. This is how I usually make use of my layers.
Lower Layer: I use this for the floor, and walls.
Middle Layer: Lay Larger Details suchs as tables, lamps, and carpet.
Upper Layer: Fine details, cups on top of tables, shop items around the shopkeeper, maybe some odd lighting.
Event Layer: Triggers, actions, characters. In here goes what really makes a game a game.
Welp, this is all I could help with considering I have a very limited knowledge of RPG XP. Good luck.