NMoasis said: What's underneath that first little bed? If it's directly on soil, I agree that's you would do best with an organic like compost. What's in it so far?
NMoasis said: Any chance you can get in there and remove the gravel and plastic? Most perennial roots will eventually grow down into the soil, even if it's clay, then it isn't shallow. I'd just dump a couple of bags of something like raised bed mix or even topsoil with some compost amendments into that little bed. A raised bed set on bare soil acts differently than containers. You've got a few different scenarios going on there.