I find that a good size for maps is 30x30 traversable area per tile on the Town Map. For instance, I would make something three map tiles wide be 90x30, or something like Jubilife be 60x60. Take a look at my attachment for an example of the former. A good size map with plenty of variation, a good amount of paths, shortcuts back, and areas for later. Note there's some custom tiles there, so don't go stealing anything.
With the tilesets problem, I think you just need to understand how tilesets and mapping works. To use the trees as an example, in my tilesets I have maybe a dozen or so tiles. Four tiles are the base and middle of the tree; I place these on layer two in the placement I desire. Then I have the edges and tops of the tree. These go on layer three wherever I have bases on layer two. Then there's the joiny bits where things would usually overlap; they also go on layer three.
Take a look at my second attachment for an example. Highlighted in orange are the layer two tiles. I start with the bottom four, put trees wherever I want them, then at any place there there are multiple trees in a line, I replace them with the top four. Then, I place the tops of the trees on layer three, and outline all of the outermost trees with the appropriate edge pieces. Easy as pie. All you need to do is make a similar setup in your tilesets using your tiles.
Also, if I may make a recommendation, avoid using DPPt or BW/2 maps as inspiration. While there are some good examples of mapping in there, there are also a lot of blocky, unnatural maps present in those games. A better source would be HGSS. Much improvement was made in regards to mapping in those games.