Black spots on tomatoes are generally caused by inconsistent watering. If a plant goes dry and then gets watered it can cause this problem. I've never grown a topsy turvy plant so I'm not sure what to tell you. In a normal garden setting, I would say to just mulch your plants so the soil moisture stays consistent and your tomatoes should do much better. In this case, I would say to be sure you water the same amount each time and try to keep rain from soaking the plant. I prefer growing tomatoes the traditional way."