Wouldn't it get tricky if you start adding plants directly to the substrate? You're going to need to water them and soggy soil sounds like it would be a big headache if you accidentally overwater. I think the hardest thing is mimicking the natural balance of an ecosystem in a small enclosure.

I wonder if it would help if you plant the pots and hide them in the substrate. Maybe that would give you more control when it comes to watering and cleaning?