This is how I arranged some tilesets, it is by no means perfect or very organized. If I felt like I was getting tight on tiles I would definitely organize it like I did the bottom right, but my main concern was to create a vast and expansive overgrown forest. This being my first attempt at making something with so many layers it is sloppy and because I know what to expect now, a second run would be a lot smoother I think. A lot of tiles became obsolete as I progressed and are still in the database just no longer in use.
I used a base maptile for my default layer, basically just grass.
Layer 1 I used the grass again, since the shadows are in the same set.
Layer 2 I used the rock formations.
Layer 3 I used the tree's outline/bridge
Layer 4 I started using flavor tiles, like shrubs, big leaf things, fruit thingys.
Hero Layer
Layer 5 I used the tree's leaves.
Layer 6 I used the flavor tiles again.
I drew everything in MS paint using the palette's colors. I like doing this because I can copy paste easily and not worry about 20x20 with any props or planned overhead tiles. I use one big file for all my maptiles before transferring them into custom.
Eventually, it will layer very nicely and you will get a nice looking place
Oh and this area isn't finished I wanted to animate some stuff. I am not sure if I want to animate the water because that is just an enormous time consumer but maybe...



