It should be okay as long as you are only adding enough to cover some roots. There is a trick to adding substrate to your aquarium using a 2 liter bottle so you don't make a huge mess, there are some good youtube videos out there showing the method. Depending on the size of the aquarium will really depend on how much you can add. If you wanted to add a lot you can easily wash the substrate, put it in a 5 gallon bucket with established tank water and a power head for a couple days, change 50% of the water and replace with tank water and let sit for another two days. This will kick start your substrate and make it "live".