I think that should be possible. But remember that you can't use more than 256 colours because the Maker is using PNG saved GIFs (at least that's how I think it works in RPG Maker 2000).
To make transparant tiles edit one of the basic Chipsets and fill the whole sheet with the colour they're using for transparency.
I'm not sure how it would work with the different layers, or if it would be possible to put multiple image layers in one map (I don't have much experience with using images in the RPG Maker XP).