Hey, I don't have a Tiled set-up but I'm working on an update to make implementing your own much easier: https://mattwalkden.itch.io/rpg-overworld-tileset/devlog/800175/update-on-the-up... . The update has taken longer than I'd expected but it's almost done, I just have to animate some new water tile variants.
As well as fixing the existing tiles for auto-tiling and restructuring the tile set for easier general use I'm going to put together an alternate version of the tile-set for single layer editors.
So all this is coming soon (the next month or so) but in the meantime with the existing tiles the best way I've found to work in Tiled is to have a base layer for grass, a layer for biomes (wasteland, snow, desert, sea etc.), a layer for sub-biomes (long grass, deep snow, deep water etc), and a layer for other features (mountains, buildings, trees). You can use multiple extra layers to overlay different elements too for more variety and more organic looking maps.