| If you are going to completely drain the tank and clean it I would ditch the substrate, or if its decent looking, I would rinse it in fresh water and reuse it (flush out the crud). You may want to scoop a little of the top layer and keep it a plastic tub with some of the old tank water to reseed the cleaned tank with.
I would do the actual cleaning with a mix of vinegar and water. An old credit card will work well to safely scrape off the stubborn stuff. | 
