Yea deff take out that green substrate. As for the bottom, most people just have the typical black square plastic insert piece as their bottom. The piece that came with your starter kit. If you always have standing water at the bottom from misting, make sure to wipe it up daily. Don't leave standing water in there. Lots of people will drill holes into that plastic piece, and have some sort of drain tray under the cage for the water to seep into. Easy clean up and no bacteria that way. As for me, I have an all-screen bottom. I just bought me a piece of Stainless Steel .020 Wire Mesh Cloth Screen online and cut it to size for my cage, then I used some clear, non toxic, weather-proof caulking to caulk it into the bottom of my cage. That way, all my water drains out of my cage and into my drain tray, yet, no crickets or any other insects can escape. His feces also stays on top of the mesh screen and that allows me to check it for problems of illness or dehydration.
Those have been known to have the pumps go out after a short time. And I've heard that they get contaminated easily. You'd have to make sure no insects are able to get down inside of it at all, and you'd also want to make sure that your chameleon isn't pooping in it. That could be bad. Although it has a filter, those don't do the job 100% of sanitizing the water. You'd have to change the water in it quite frequently and take the unit apart and clean it from time to time as well. Otherwise, it's the same water re-circulating over and over in the same fountain. Although any type of waterfall and such is usually not recommended, I believe that with daily or at least every-other-day cleanings you could be okay. You want to get your chameleon used to drinking droplets off of the leaves and such in the cage though because as with all things mechanical, that cantina won't last forever. Your cham will need another water source at some point. Also, eventually you will want a bigger cage and live plants are deff recommended as they hold water really well and provide extra humidity within the enclosure. What you have right now for starters is okay. Just keep adding to it and saving money for things. Chameleons are expensive! And don't ever hesitate to ask the community here for help. Lots of really good and knowledgeable people on these forums.