Well, Dependent on how big the tank is. If you get a thick hose and use it as a syphon; suck up all the rocks with it into a bucket. This will remove the rocks and quite a bit of water so you can change substrate and do a waterchange at the same time. The thicker the hose, the faster it will take out water. A 1 and a half inch hose can drain a 10 gallon tank in less than 3 min.. So be careful you dont drain the tank completly. If thats too much for your tank; just get in there with a cup or something and scoop away!
It is advised to remove fosh during this process regaurdless of the method you use