Sounds good. Over time, it's likely that the layers will mix together, but there's nothing wrong with that. The fluorite I have is sharp, so if you have bottom feeders like cory cats or loaches you might want to look into the more granular form of that substrate.
When I prune plants I tend to just cut the tops off-- however long I need to. If it's a stem plant I tend to cut the stem just above the growth node. If it's a leaf or rosette plant I either take a whole dying leaf out or trim the tops off.
EDIT: I forgot to ask you: are you planning to plant the tank with the Silver Dollars? They're herbivores and will tend to eat most aquatic plants.