I lay mine out like this... (top to bottom)
-Trapped fortress-
surface (in 4 corners, 3x3 stairs down)
dirt:tree farm / central staircase waterfall source
dirt:n levels of paths down to main entrance
first rock layer:traps to entrance & depot & initial storage + animal "pasture" also top of dump chute, 3x3 halls from four corners of surface to central staircase
5-9 layers: dump chute / mining area for ore
: bottom of dump chute / mining area for ore
: crafting stations / mining area for ore
: stockpiles 1 (20 x 20 each, four adj to central staircase / mining area for ore
: stockpiles 2 (20 x 20 each, four adj to central staircase / mining area for ore
: magma smelters and forges (8 of each) plus stockpiles of ore to be smelted
: magma "room" to power smelters and forges above, mining area for ore
: empty due to heat from smelters, mining area for ore
: dining hall, wells (3), farm
: hospital, well-water-source
: empty due to water above / mining area for ore
: mayor's rooms, each 20x20, three of them, all 3 width halls. bed,throne,dining
: apartments, 5x5, 8 in a row, four rows, three width halls
: apartments, 5x5, 8 in a row, four rows, three width halls
: apartments, 5x5, 8 in a row, four rows, three width halls
: apartments, 5x5, 8 in a row, four rows, three width halls
: apartments, 5x5, 8 in a row, four rows, three width halls
:: mining to cavern top + drain for cent. staircase waterfall to map edge.
: single floor tile covered into top of cavern for spores to grow trees.
:: 3x3 stairs down to candy & clowns.
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this has worked pretty well for me to funnel all the invaders into my traps. i use a slightly different layout when dealing with the great goblin melter, as it needs 5 layers and a nearby volcano, plus water for logic, etc.
I've gone with a very vertical design to keep the paths short. it generally doesn't take more than 25 levels, which is easy to do with worldgen. I keep the whole thing between embark -2 and the top of the first cavern.
consequences of this: i have nothing on the surface except four stairways down, one in each corner. In fact the surface/embark is not part of any active burrow unless a migration wave goes badly. I have no sunlight crops. I don't typically have any surface growing trees in the stockpiles. But it's defensible!