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I would give the tile map an overlay layer or several, depending. Have the base terrain tiles and then plop some building/resource/unit transparencies on top to allow the terrain to be reused.
[0,4][1,4][2,4][3,4][4,4][0,3][1,3][2,3][3,3][4,3][0,2][1,2][2,2][3,2][4,2][0,1][1,1][2,1][3,1][4,1][0,0][1,0][2,0][3,0][4,0]
function drawObject ($file, $x, $y, $z){ $map [$x][$y][$z][] = $file;}
drawObject ('grass.jpg', 2, 2, 0);drawObject ('house.png', 2, 2, 1);drawObject ('player.png', 2, 2, 2);
$map = array( 2 => array ( 2 => array ( 0 => array ('grass.jpg'), 1 => array ('house.png'), 2 => array ('player.png'), ), ),);