Wouldn't worry about adding the old gravel in for bacteria. They're sessile so having water drain off of your old gravel and into the tank will not do much. Your filter should have most of your bac anyways, unless you aren't running a filter.
When I substrate change I drain the tank down to 10%, use a perforated scooping device to remove it, suck out the last of the dirty water and then add the new stuff and set the tank back up. It's pretty hard to go wrong with the tank itself, just make sure the fish and filter are taken care of.