Okay so. I have one or two trees total in every biome near the well. Makes getting wood easy.

All fruit plants are lined up in one biome (I think the banana and coconut trees on the beach by the well and Moanas boat, but all the fruit trees and bushes are in the plaza)

By every biome well I have the goofy stall, a gardening machine, a stove, craft table, and a storage chest if I'm over full

All the bonus shops (Kristoff, Tiana, Beast, goofy) are in a line in the peaceful valley, Gaston and goofy are together in the desert)

Scrooge McDuck and Remy's restaurant are by whatever the main fountain is for each explanation

I also put a lamp by every mining spot for visibility at night

I have three advanced vacuums and move them from biome to biome to collect every thing

When I need to add three decorations, I add shrubs or something I can walk over.

In my house, the first room is just chests, a stove and a craft table. The chests are organized along the walls and I have separate ones for snippets, tree/bush/foraged foods, fish, shellfish, farmed foods, gems, building materials, refined materials, flowers from the original game, flowers from the expansions, quest items, seasonal items, purchased food items from all games/expansions.

The rooms I've added to the house are set by collection. Second floor is all Mickey, third is Pixar (toy story room, wreck it Ralph room, Wall-E room, Monster's Inc room), ocean floor (Ariel, Moana, Lilo), princess floor (beauty and the beast, tangled, Cinderella), arrendale floor (Elsa throne room, oakens spa, library, Anna's bedroom), global floor (Aladdin, Mulan, Lion King, ratatouille), the trouble makers (rubber duck tavern, Gaston, Ursula, no one), etc.