What I do is try not to get fixated on one level or area, but jump around. Now, I'm a very abstract thinker. So it helps me to think in abstractions, then generalities, then details. No matter how you think about it, though, you need to separate your goals from how you achieve them.
For example, my
goal might be to have about 3 major factions in the area, largely in a stalemate, but sniping at each other, and maybe several more minor factions or capable NPCs complicating matters. (Note that we aren't set on 3 major factions or the exact mix or numbers of the minor entities.) Or more accurately, my goal is to have an area where a lot is going on, and the PCs going there is almost assuredly going to stir things up, which they can try to manipulate when so inclined, interact with otherwise, and occasionally suffer fallout from even if they try to stay out of it. I just know from past experience that 2 major factions isn't enough and you need some complications to make it come to life. If I happen to develop a 4th or even 5th major faction when I get started on the details, so much the better.
From there, with the goal set and the abstractions already started, it's easy to start drilling down. Faction 1 is perhaps the powers that be, has a lot of overt control, operates mainly in plain view, and has considerable traditional resources (money, guards, etc.). OK, fine, once you state it that way, just throw some NPCs and whatever other mundane and fantastical things you want to include. A lot of it is easy: Faction 1 has competent but not spectacular soldiers, supported by common militia, and with a typical NCO/officer hierarchy. Stat appropriately, even if just reskinning something out of your favorite source. Details are about naming things, giving numbers to it, locations, and most importantly, personal goals and motivations to some key individuals.
However, don't get too caught up in finishing Faction 1--unless you are really rolling with it. Slap out all the stuff that comes easy, note gaps to fill in later, and leave room to change it. Then start on Faction 2 or minor complication X or whatever is readily at hand.
Let the feedback loop happen: Why do you include a sour but capable mage who tries to stay aloof from all the the turmoil, but keeps getting dragged into things, and will both resent the PCs from dragging him in, but is also somewhat resigned to it from past experience? Is it because you had the idea for the character and wanted to include him since you had it? Is it because you thought that an NPC with those motivations filled a hole in your GM arsenal? Is it because your mind jumped around when thinking about how Factions 2 and 3 have been clashing lately, and the NPC emerged out of that? It doesn't matter! The feedback is churning, your gut sent you in that direction, and now you've got something to work with. Worst case, you'll put together the NPC, have some ideas for it, then decide not to use it or the players happen to never meet him. That's OK. You got him for almost free and a few minutes of note taking, and he might be handy later.
Again, this is how I do it, and how I think about it. There's no plot. There's creatures with motivations and goals and plans and details in a situation that is either unstable or likely to become that way as soon as the PCs start doing stuff in it. Then when something happens, I think about what the creatures would do about it, and go from there. I just had this happen fairly dramatically in a game I'm running. The PCs managed to kill at lot of the nastier wandering monsters in the area, bloody the nose of the local goblins, and snipe at a tribe of strange creatures from the nearby swamp. The area had been in a rough, low-combat stasis for some time, which is now disrupted. I thought about it, assigned some odds and rolled. The upshot is that the goblins are pulling in heavy reinforcements from their main base. They are doubling down. The swamp tribe is pulling back and observing, hoping to get some easy prisoners by stealth and picking off stragglers. The tough wandering monsters being temporarily killed will allow more movement of the remaining wandering creatures. The bandits in the area had already pulled back to their base, taking their treasure and captives with them. Which is a problem for the PCs, since one of their main goals is to rescue those captives.
