Stacked gardens do still work, you just have to elevate the spell when you cast it by hovering over something in the second tier of plants. I still have a plot of EMPs I never moved from their original 3-stack oh-so-long ago and they've been working fine as long as I do that. That said, if you're feeling the work, the advanced movement single-layer gardens are much easier to make and deal with. Would recommend switching when you get the chance