I don't really think layers have anything to with walking on events. The main thing to worry about is if they are set to passable or unpassable.
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THIS TOPIC HERE.
Go to the question, I have problems with my map. The player can walk over solid stuff. How do I fix this?.
It may not seem like it, but that can help. If it STILL doesn't work, go into the Database (in RMXP), into the Tileset Tab.
Here you can set the passabilty levels of each tile you see there.
O means the player can walk over it.
X means it's the same height as the player.
If it still doesn't help, then post the demo.