I have multiple companies:

Parent Company
--Company A
--Company B
--Company C
--Company D

I also have multiple warehouses:

Warehouse East Coast
Warehouse West Coast

I've done some test setups with different ways but I still haven't found what works best. I don't have any shops and products are sold directly from the warehouses. Each company uses both warehouses and their locations are also inside each warehouse. The warehouses serve only as logistics for the nearest customers instead of nearest shops. So Customer on West Coast will ship from Warehouse West Coast.

How do I set up this structure?

The documentation makes it appear as though I need to setup my locations like:

Warehouse America
--Warehouse East Coast
--Warehouse West Coast

But I don't see how this affects the way things work? It also keeps talking about shops and setting each shop to a specific warehouse or a warehouse is only company specific. Since all companies use the same warehouses, this doesn't seem to apply. in this case.