How do I properly make use of the TileMap when it's hard to see how all parts connect? And how do I account for objects to place ontop the tiles?

Help
1

1156-SLYNYRD-Pixelblog-98-Player_Sprites34
1156-SLYNYRD-Pixelblog-98-Player_Sprites345120×2560 72.6 KB

This tree for one, probably can’t be put ontop of a Tile without breaking things

I am not sure how to also keep track of how the tiles connect properly, either

2

create another layer, or another tileset only for decorations.