Your black tank is a holding tank, it is not a septic tank where you're going to let things sit for long periods of time while the chemicals break it down. Drain it and be done. Flush it if you want, it's still not going really be any cleaner or smell any better.
If you want to use the product that's your option, but don't worry about leaving the last 1/2" in there, just give the toilet a very long flush and then add the product.
This product is mostly for "city" people who have never built, lived with, or used a septic system.
Bill