After you flush your liver . Or, as IntutiveGal said, you should try to do some bowel cleansing first. If you do not have a clean passageway for the stones to exit, then they can get caught in the colon or small intestine and cause a lot of problems as they are recirculated through the liver.
To be honest, I really would recommend you doing a bit of bowel cleansing first. Many people become WORSE, or their symptoms become worse when they flush and don't follow it up with colon cleansing via an enema or colonic.