Do you think your encounter design structure is appropriate for small location based concept? Say a small, low lvl undead village (five houses and a church)? Should I design the whole village as one encounter (DQ: can the players figure out what happened?), or break it up into multiple encounters?
I think my encounter design structure is appropriate for ALL encounters. All of them. That is why I said in http://angrydm.com/2013/05/four-things-youve-never-heard-of-that-make-encounters-not-suck/ that you should ALWAYS F$&%ING USE IT.
That said, how you use it is up to you. You can have a big thing like a broad investigation of an entire area be one encounter or you can break it into multiple encounters if you want to break the investigation down into multiple goals. For example, if the encounter is about piecing together what happened, you can break that down into several different clues, scatter them around the map, and put encounters in the way of some of them (where others might just be freebies). In the end, it will have a different pace to it. A different flow. Using the whole thing as one encounter is like a montage scene, spread out over a long period of time. Having multiple encounters is more focused on the exploration and bouncing from encounter to encounter. Either way is perfectly fine. It just depends on how you want it to feel.
Also, ask yourself whether this village is minor and only deserves a single scene to set the tone of the mystery or whether you want it to feel like an entire act in the adventure.
That said, how you use it is up to you. You can have a big thing like a broad investigation of an entire area be one encounter or you can break it into multiple encounters if you want to break the investigation down into multiple goals. For example, if the encounter is about piecing together what happened, you can break that down into several different clues, scatter them around the map, and put encounters in the way of some of them (where others might just be freebies). In the end, it will have a different pace to it. A different flow. Using the whole thing as one encounter is like a montage scene, spread out over a long period of time. Having multiple encounters is more focused on the exploration and bouncing from encounter to encounter. Either way is perfectly fine. It just depends on how you want it to feel.
Also, ask yourself whether this village is minor and only deserves a single scene to set the tone of the mystery or whether you want it to feel like an entire act in the adventure.