First, I made a tile by tile map of my town, marking only the permanent parts: the rocks, Train Station, Town Hall, Plaza, Retail, river, ponds, my three player houses, and the Caf? + Police Station, which I had already built.
View attachment 163221
Then, I marked my villager houses, but only the one's I know I'll be keeping, and started drawing my paths and bridges on that map, while marking them out on the game by surrounding the path with flowers, since I want a natural dirt/grass deterioration path, the flowers help it stay where I want it). This is when I started cutting down the trees that were in the way, little by little until I got the golden axe. I tried to stay consistent: 1-wide paths only were it lead to a house, 2-paths for the most part, and 3-wide only where I wanted to align it with something (the town tree/main street entrance).
View attachment 163222
Then, finally, I started planning my trees, shrubs and PWPs. You'll find this guide very useful for figuring out where PWPs will or will not fit:
https://s-media-cache-ak0.pinimg.com/564x/6c/4f/32/6c4f322011cc08b71dee833148a23330.jpg
The red tiles are the project's actual size, the yellow is the free space that needs to be around it (where only flowers and items can be placed, no threes, shrubs, other PWPs, not even the PWP's yellow areas can overlap). The blue tile is the one you need to be standing on when talking to Isabelle.
View attachment 163223
I still don't have all my dreamies, but I think I still have a lot of free space to move them in. I'm not crazy enough to plot reset for a "perfect" location, I just try to place them out of the path I already planned.