For really scrubbing out a cc substrate or a tank in general for that matter, nothing beats one of these:
http://www.diatomfilters.com/
Just stir the substrate up good and leave this guy running in the water. Will suck all the nasties right out of there. When you are done, you can backflush the filter in the kitchen sink and have it ready to go for the next time.
Be advised that there is some concern these devices will trigger a
diatom bloom since they rely on diatomaceous earth to operate. My humble feeling on this is that as long as the filter bag is used properly, that is not as significant an issue.
If you do get one, you can get diatomaceous earth refills much cheaper at your local pool supply outlets.
Hth!
Dan