Try to avoid stagnant pooling of water, as it can lead to more mold/algae growth. The soil being moist is enough to grow the roots. And if you're worried about the back slope not getting enough moisture, you could put something under the front of the tank to tilt it back slightly, so the water settles in the back.
The tank should be covered to keep humidity but let it air out everyday for like 10 mins to circulate fresh air, or you can cover it up but leave a tiny opening in the corner. Depending on the ambient humidity of where you live, you should be able to find a method that works best for you. I live in a very dry area, so I did the 10 min air out rather than leave a small opening. And my photoperiod was 12 hours for maximum growth.
Not really sure about the fungus on the bonsai though, so can't say much about that.