My way is probably so strange as to be unhelpful, but here goes:
I build my forts to run on magma, and as such I build their lowest layer just above the magma sea, taking advantage of a peculiarity I've noticed where natural rock spires down to the semi-molten rock form where the corners of the map cells meet--I use the bottom of one of those spires as a form of sump, and dump magma waste from the defenses into the top of one of the map cell magma caverns, placing all my inlets down in the spire to ensure an adequate supply as it's refilled from the map edge; an adjacent such spire becomes the lowest point of my fort proper. The rest of the fort grows up from there, with its top at the third cavern layer for easy access to wood, muddied rock, and cave moss; I drop tiles of clay and sand to the fort level for easy access and the shafts dug to allow their fall become reservoirs of magma and water and from then on ignore the surface except to gather animals for use in !!SCIENCE!!.
With that as my goal, I tend to try to find a length of rocky cliff to use as my fort entrance to avoid having to pave over dirt to prevent tree growth in my entry corridor, preferably one on the same cell as my eventual magma trap entrance. From there I just dig/build organically and usually diagonally down through the caverns, digging a short exploratory tunnel where I suspect a spire adjacent to my planned fort location to be in order to properly align the magma trap/entry tunnel. At the end of that, I start constructing the staircase for the fort itself; the magma sump goes in the spire at the beginning of the tunnel. It's worth building a temporary fort in the pre-cavern 1 section of the tunnel and an aboveground farm in order to fuel the digging of what is certainly a needlessly complex entry tunnel.