@antimatter,
There are methods, the alpha method is one. Should be able to find info on the method in any good pile foundation design book. There are also methods discussed in various FHWA publications.
As for the length of the shaft capable of developing resistance, for straight shafts, I always use the full shaft length. For belled shafts, just the portion a couple of bell diameters above bell. Many times the capacity is controlled by the cone of soil weight that can be mobilized. Doesn't do you any good to develop the skin friction if there isn't enough soil weight to resist the friction.