Step #1 View pictorial step by step instructions to set the stem angle to make sure you are sitting on your sit bones. Riders that extend too far to reach the handlebars will lift their sit bones off the saddle. Many of these riders will misdiagnose discomfort with a saddle issue. Instead bringing the stem closer to the shoulders will allow the rider to sit on their sit bones and will solve most comfort issues. Follow the remaining steps to optimize comfort.
Step #2 View step by step instructions to set the saddle angle so that it will be level under compression of the riders weight. If it is not very comfortable you should set downward angle on the saddle not more than 5 degrees. Saddles that have an upward angle will almost always feel uncomfortable. Additionally, with a large downward angle ( greater than 10 degrees ) the rider will slide down the saddle while pedaling causing discomfort.
Step #3 View step by step instructions to set the seatpost height. The riders leg can never be completely straight while pedaling, this may cause cartilage damage if ones leg gets locked in the straight position. Additionally ones leg should not have too much of a bend while riding. A large bend at the knee will make pedaling hard, and will not be good for ones joints ( it is highly likely to cause knee pain ). At top dead center, the furthest pedal position from ones hip, the rider should have a 30 degree knee bend at the bone ( not at the surface of the skin ). The ride will be amazingly comfortable once the seatpost height is properly set.
Step #4 ( Part of an advanced setup ) View step by step instructions to set the saddle for aft position. When the pedal is in the 3 o'clock position the rider should have the bottom of his/her patella tendon directly above the ball of their foot. If it is not properly aligned push the saddle forward or back until it is properly aligned. This will set your power stoke, so you will ride with as much power as possible with minimal effort.
Step #5 Adjust the brake levers. The brake levers should be placed on a straight line emanating from ones shoulder. A common problem is sharp bend at the wrist, which will cause wrist pain