I went through all the cards and tokens from all the Eldritch Horror expansions and split them out. I shuffled all the location encounter cards into their decks. They can all stay as they are no matter what boards I am playing.
All the standard Ancient Ones get their cards stored together. The two Ancient Ones specific to the Antarctic and Egypt are gathered with the location encounter cards for those boards. There are also some adventure cards that go with the boards (e.g. the Museum Heist from Egypt), so these go with them.
I decided to keep all the preludes in one deck, even though there is a specific prelude for each of the two boards. I think the mechanism is that at the beginning of setup you draw a random prelude card and if it is the one for a add-on board then you use that board. (You can also pick an Ancient One if you want to use a particular board).
The gate tokens for the add-on locations go in the add-on piles.
All the smaller cards, items, artifacts, relics, spells, etc are shuffled into their decks. These all go in the main box.
It all didn’t take too long, and also gave me a opportunity to review the rules for some of the newer mechanics (such as preludes and adventures). I had to understand them to decide where the cards belong.
Now, hopefully, when I come the play next it will be simple to find everything and setup and should save a lot of time.