I dig usable rooms around a central staircase or rampway. Mostly central staircase, that is, as I tend not to use up/down stairs until the lower levels. Usually I favour at least one additional stairway that also runs through most of the fort, as an alternative pathing solution. Danger from surface enemies is met by way of a drawbridge that is constructed as soon as possible - spent too much time playing DigDeeper and coping with orcs sieging in the first year.
In current fort, defense against cave critters is met by way of a small drawbridge that guards the only open accessway into the caverns. All other routes being blocked by walls. Uncertain of how well this works, or if raised bridges still work like constructed walls against buildingdestroyers.
The depot and woodstockpile is usually on the first layer dug into; including the food stockpile if there's soil at surface level. If not, food stockpile is placed near wherever I place my farms. Crafts workshops are built one level below the depot, directly sprouting off the main stairway, with a stockpile of stone for stone crafts and a stock pile for finished goods, plus 2 workshops, all in a 10*10 room. Usually the carpenters, masons and mechanics are placed in a 10*10 room on this level as well, with a stone stockpile for the masons/mechanics. One level below that, a furniture stockpile that is a minimum of 10*10. Refuse stockpile wherever I feel like placing it. Food workshops either on same level as food stocks, or one level above or below.