Just run your filter from your holding tank on your main tank until you need it, then move it over to the holding tank... that way, you don't have to worry about ammonia, as the tank will be essentially cycled. I'd much rather do water changes than rely on a chemical to remove ammonia, but that's just me. If you have made your mind up on using it, you can put some in a mesh bag of some sort and put it in your filter.
"What, exactly, is the internet? Basically it is a global network exchanging digitized data in such a way that any computer, anywhere, that is equipped with a device called a 'modem', can make a noise like a duck choking on a kazoo." - Dave Barry