It is quite simple if the bike saddle is not comfortable then you won’t sit correctly on the seat. If you don’t sit correctly on the seat most of the time you will create excess pressure in the lower back which in turn will cause shoulder pain and potentially knee pain, from not recruiting the glutes.
The pelvis has a hole in the bottom of it through which all our tubes come out, it is a sensitive area – if you were to sit straddling a bar or branch of a tree on the middle of your pelvis it would be painful, which is essentially what happens with many bike seats that are narrow and hard.
It is important that the pressure and load of the body is bearing down on the bones of the base of the pelvis, not the soft tender tissue that spans across and between the seat bones. This is why more and more saddles have a hole in the middle – to alleviate the pressure off the perineum area. Pressure here can create pain down the legs, numbness in the area or around the area and also refer pins and needles or numbness down the legs. Old school saddles were narrow and aerodynamic which was not comfortable.
Some saddles have a wide back, providing a place for the seat bones to rest, and are sold as better for your back, which they may be if you are just tootling around, the problem with these are that as the foot goes to the bottom of the stroke the hamstring tightens and the muscle becomes firm and this hits the edge of the seat which pushes you forwards off the front of the saddle, which can be quite annoying to keep having to push oneself back onto the saddle.
The other issue with an uncomfortable saddle is the lower back strain and shoulder strain due to the pelvis being vertical and not at a forward tilt in line with the spine. This can be seen quite clearly with the pictures below, not only does this cause the back to buckle up and so put a huge load on certain lumbar vertebrae but also it causes a loss of power into the wheel – if you push down hard into the pedal and as you do the core gives and the lower back slumps backward then there is less energy driven into the pedal arm and drive train and into the wheel. If the core is strong and the pelvis remains static then as the leg powers the pedals the energy is directly driven into the wheel, which translates as better speed forwards.
So the best solution is to have a saddle that has a better taper form front to back and is narrower, but wide enough to sit on the seat rim of the pelvis and has a hole in the middle where the delicate tender soft tissue of the perineum is to avoid pain and discomfort.
Here are some good links to great saddles to ease discomfort in cycling.