All my containers are side-by-side so I'm going to keep that style, but when it comes time to build a second level of containers, I'm going to build a 2nd floor and not just stack it. It takes up more space, but it also gives me greater control of my layouts.
I normally multi-level my foundations, as in 3 stacked [8x2] blocks. I do this for "under-floor" conveyancing ( the middle block is removed ) which allows me to get around without having to jump all over belts and such.
I has a plan! *King Julian accent*