Try just moving some of the substrate to be thicker in the areas you need to get the plants rooted. You can always add some more later when you have more funds.
Are you just cycling the tank right now? No fish? Sounds like it could just be a work in progress for a while if you need it to be. You don't need to worry about draining the aquarium. Everyone does pruning and adjustments etc once filled.
As far as discus goes... Do you know a lot about them or have much experience with aquariums in general? I know they need really particular water parameters and are some what delicate in that regard. Also ... Your substrate can affect the ph of your water or its buffering capacity. I don't know about fluorite in particular but I would definitely do a lot of research bc they are ph sensitive.