Yeah I have no idea what you did - what other pieces, where the entrance is, how things are clipping...

I can tell you that without any existing structure if you want flat to ground vs half raised you can chuck down a wooden floor piece and sort of snap the stone into the edge of that to get it ground level instead. Which itself may not be pretty, there's a good chance dirt will clip through - especially since snapped stone sits lower than wood.

But I have no idea if that helps because I don't understand the problem.

If we ignore clipping and existing structures, you might be able to get the height you want to digging the ground, placing the stone, and raising/flattening the ground again - so that everything is where you want it. No idea if that's possible in your situation.