Looks like you are using a very organic mix to plant those in. There are as about as many opinions on soils/mixes as there are bonsai practitioners in the world, but the underlying point to all of them is that for the best health of the tree it needs to have good drainage. No standing water on top of the surface, no pooling in the bottom of the pot, etc. That will lead to a lack of oxygen getting to the roots, then they rot, then the tree dies, and then you are sad.
So for those wood boxes you've made, make sure to drill plenty of holes in the bottom and lower part of the sides to let water out and air in. Its good that they have feet to let air move under but make sure there is plenty of drainage holes too. Add holes to to the plastic ones as well to help them drain as best as possible.