Hi
Generalized answer for comment-faq:
Core structures like houses, cliffs, and trees are featured in the promo screenshots to provide visual guideposts.
I arrange the tiles in logical groupings as best as I can, but some might be tricky to place, especially some of the variant tiles. The sets are arranged with a focus on flexibility that makes use of alignment-precision (it's why these sets take a long time, tilesetting is a whole thing beyond the textures themselves).
This kind of tileset isn't just for use in RPGMaker, but for any engine or tool that uses tiles in a regular grid (there should be a master-sheet for general use in addition to the RPGMaker-formatted sheets).
I'd recommend simply "playing with them" in a way to get familiar with maximizing the tile-palette, because that will develop your own language of tile-clusters, which makes your mapping process smoother and more intuitive (and more fun) in the long run.
On the other hand, if you're not making bespoke environments, (doing something procedural for example) a lot of the variants and edge-case tiles might be unnecessary (designed for hand-placed details), so it'd really depend on the specifics of your project.
Specific answer to you:
Sounds like you're doing something more complex than regular drawing with the tile-palette, I'm happy to help but would need some more individual specifics.
Please send me an email (finalbossblues.com/contact/) and then we can share image attachments easily, if I can see the context of what you're doing, and then I can help you directly.
Thanks!