Hi! So not counting the player/npc layer, I used 7 layers to create the Town in the images above. Below I explain how I used each layer and how to perhaps reduce this layer count:
7) Overlap Layer - Roofs, Tree Tops, Boulder Tops, Town Wall Top(just the upwards facing end piece of the Town Wall) (This layer allows the player/NPC's to appear to move behind the buildings, trees and town wall end-piece. It also allows things like fences to reach be behind the buildings, as well as the Town Wall end-peice to over lap building walls and cliffs. If you don't need this, then you can place these on the Big Solids Layer and skip this layer.
<--- (Player, NPC layer would go here)
6) Details - Rocks, Boulder Bottoms, Fallen Log, Berry Bush, Crates, Barrels, Fences, Fences, Water Lillies, Floating Ice, Signs, Wheel Barrow, Stair Entrances, Wells, Chest.
5) Big Solids - All Building Walls, Town Wall, Stone Deck, Stone Stairs, Tree Bottoms.
4) Cliff Walls (Cliffs can also live on the buildings layer if you are okay with some placement limitations)
3) Shadows (Alternatively, you can create ground tiles with the shadows baked into them. But to create the porches you see in the images above you would have to add the shadows to the wooden deck tiles as well. This will increase your total tile count by quite a bit, but allow you to remove this layer and still have porches with shadows).
2) Floor/Ground - Ground, Grasses, Flowers, Snow, Melted Snow Patches, Wooden Deck, Wooden Stairs, Paths, River Banks.
1) Water - All Water Tiles
I hope I got all that right, but if something doesn't make sense, let me know and I'll try to figure it out! :)