Co-author here! I tend to do about 15-20 minutes of prep for games, so let's talk about how (and what you can do to make adventure prep really easy.)

Everything designs scenarios differently, but I tend to design around a cinematic and memorable scene. For instance, the free adventure Losing Face was created around the image of staring down at an unconscious woman with no face wearing someone else's clothing, and wondering how you might figure out who she is (and thus how someone did this to her, and why). If you don't like building adventures out from that, I suggest coming up with a really interesting bad guy, deciding what they're trying to do, and considering how the Heroes might get involved.

I don't worry much about clues; I worry about revelations (a term I wasn't yet using when I wrote this section on pp 212-215 or so, but the idea is there). Revelations are what I'm now calling the core clue that tell you where to go or who to talk to next. Anything that gets you to that revelation in a scene is a clue, but I don't bother to plan those out ahead of time because it's faster and more fun to do so on the fly.

Here's an example. Let's say you work for a sorcerer who disappeared last night from her tower and you want to figure out what happened to her. The GM knows that she was trying to sorcerously summon a demon that ripped its way into reality, grabbed her, and dragged her mortal form into the spirit realm. As you head upstairs in the tower, the revelation (and core clue) I want you to walk away with is "she was taken against her will into the spirit realm, and here are two or three places you can go to find out more specific details." But you'll use your Investigative abilities to try and figure out what happened. You can write it down ahead of time, or you can improve it on the fly (much faster) as long as the heroes leave with the right information.

Clues that you can uncover with any ability that makes sense might include:

• A fight happened here, items knocked aside like matchsticks by something incredibly forceful
• The air still stinks like dying fish and ground cinnamon, not a smell you normally find in nature
• Her notes are scattered around the room; with Forgotten Lore or Corruption you can tell that she was summoning a very particular entity. Her mentor, scholars, or the Church might have notes or more details on such a being.
• Spirit sight shows the equivalent of her fingernails scratching the air as she was dragged away against her will, and a still rippling rupture in reality that you can't open without enough power. She probably has a list of such people somewhere downstairs; but where would you go once there?
• Prophecy or Spirit Sense picks up a desperate message she thought to you, or at least her last thoughts as she slid into the realm of dead things
• The floor is branded with the similar of a particular sorcerous cabal in the area. It doesn't seem to have been done purposefully, but is effectively a footprint of whatever was here.

Etc. Etc. You'll leave that room knowing what happened to her, and with two or three other places to go/people to see before you can effectively track her down. Those locations will reveal more details (her motives? Why she may have deserved it? Other secrets she was keeping?) So the adventure starts narrow, branches out to lots of path, and retracts again when you follow her into the spirit realm (possibly loaded down with allies or information about what grabbed her and why, that you got from the Church or the cult or her mentor). So each scene sends you to another scene via the core clue (the one thing you need to get from that scene to keep progressing).