In tandem with gravel cleaning, it's important to siphon and replace around 10 to15 percent of total water from the tank weekly. Most gravel vacuums act as water siphons as well, so you can usually conduct both processes more or less simultaneously, saving you not only time but money, too.
In terms of replenishing what's been siphoned out, the most important rule to remember is that new water must first be de-chlorinated before refilling the tank. This is necessary in order to avoid destroying nitrifying bacteria or damaging the fish themselves. The process can be easily achieved by adding special drops (available from most pet stores) to the H20 before adding it back in to the tank. Also, when refilling, be sure to leave some space between the water line and top of the tank for oxygen exchange.