mmm - some clarification required. Do they not appear when you're still making the map, or when you're playing the game?
Tiles placed on the middle layer will cover tiles placed on the bottom layer. Tiles placed on the top layer will cover tiles placed on the bottom OR middle layers.
Is it just that you can only clearly see the tiles you're placing on the top layer? In that case, go into View and uncheck the Dim All Other Layers (I usually leave this checked so I know what's where).
If your problem is when you're playing the game, rather than when you're in the editor, I'm sorry - I have no ideas.