I generally design around a terrain for the surface portions of a fort. I usually also make my gateways 3-wide for wagon access, and when possible, mount floodgates (+mechanisms) on those doors and rig a trap setup nearby or within. It would most likely also have a nearby mini-barracks for defense, and fortifications would be available as well just in case. Factories and farms stay on the sandy/loamy areas. But with clay loam being a resource we can use now, I may have to change up a bit (and also use clay walls or make clay huts for the farming districts (up and down)).
Also if/when possible, I also make a back door with similar setup. I think (Old and maybe New) Wavehandle is one of my better examples of how I plan. Bloodfist (the fort, not the ship) as was just a disaster that eventually got corrected when I, and my dwarves, got around to it.
Eventually I would build Cap Towers (named because they look like mushrooms) around the perimeter, and setup my defense network around it with a sub-barracks between or in the middle of the network.
Of course, before I get around to security networking, I have to get around to claiming my region, IE- building a perimeter wall around the site to funnel everyone from the outside to either the front or back door.
After enough time, I eventually build a bridge system to direct everything to either the front door, or the security trap sector. The back door will be heavily guarded with cap towers and a lesser barracks, and will generally be a source for much fun when sieges come around, unless they don't bust down the doors, and re-route to the front and trap sector, unless I set one up at the back.
With recent 31.xx experience, I may need to work on making separate shaft portals from surface to underground levels 1, 2, and H). The deeper, the more interesting the building, and the more security traps for the beasts that come out (in case my gatekeepers get killed, or the doors bust). I may or may not have separate burrows setup for the individual sectors (also why I use the tomb-like portals which go directly to them; those burrows will be dedicated cavern layers, and treated as separate fortresses, since the separation would be sufficient enough to qualify).
For what it's worth, I think pitting those portals near the barracks would be most suitable. That way, the guards can worry about the back door (most likely not raided as much), and anything that sneaks out of the caverns, or to stand guard from anything that gets past the portals' trap systems and the UG forts themselves.
Regarding Isoforts (Isolated-Fort) (basically, a location like an island where I am guaranteed no contact from the outside or sieges (or is an equally safe location)), I instead build my Isofort with a city-like infrastructure; starting with the underground sewers/subways, and after breaching a(round) aquifers, mine and build the city up. Clay will work wonders with regards to some of the infrastructure, as well as easy materials to gather (unlike stone that requires breaching aquifers (through or around; I depend on DFhack for that issue).