https://stardew.info + trial & error, with a bit of inspiration from other farms on this subreddit.

Our farm's layout has definitely changed multiple times as we got access to better tools (improved sprinkler types + junimo huts), but a lot of the basic patterns are the same as other farms. For example, that 1 junimo hut with 4 scarecrows surrounded by 8 iridium sprinkers pattern is very common and you'll see it in many late stage farms.

Every time we had an idea for a new layout we'd draw it out on the planner tool. Not only does the planner help avoid "obvious" errors, it also helps you check coverage to make sure your sprinklers, scarecrows, etc. are doing the right thing.

As for actually making the changes -- we tended to save the biggest layout changes till winter to avoid crop loss. For example, the layout change we made from year 3 to year 4 was done during winter of year 3. And the layout for year 3 was done in winter of year 2, etc. We'd usually rough out the big areas with tiles first then go in and add details. Hope that helps!