I agree with some of the posters about not clearing your house if you know a bad guy is inside the house. Even patrol officers will surround and call-out if they know for sure. However, there is a problem, what if you have a split floorplan with kids on one side of the house and you and the wife on the other? Do what you got to do to protect your family. If you've got everyone in one room, get low behind something solid, get your gun trained on the door, call 911 and wait.
If you've got to clear the house, unless you can turn all of the lights on at once, keep the lights off. . Then move as slowly and quietly as you can, use your flashlight only as needed (intermittedly as you clear as not to completely telegraph your position). Stop frequently and listen. Depending on what you hear, consider challenging any intruder with loud verbal commands like, "Get out of my house, I've got a gun, I will shoot you, the Police are on the way." If you've got him pinpointed somewhere, create a little distance, get cover, get low, and challenge him out. If he does something stupid, solve the problem appropriately.