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i take it that this your first time using rmxp?
no problem, you have to learn some how =D
when you load a tileset into the materialbase, click on the color in the backround, in your case i believe it is white. click that with the left button on your mouse. that sets it to transparent.
layers are exactly what thery are called. layers. when i do it, i use the first layer to put down grass, trees, walls, etc. then 2nd layer, tables buildings, tree tips, bushes etc. then 3rd layer i put books on the tables or lil things like that. 2nd layer overlaps 1st, and 3rd overlaps 2nd.
any questions? pm me. i hope this helped =D