you may use <<Qiagen Taq polymerase kit handbook for PCR>> for your reference. this handbook has useful information for optimizing PCR procedures.

my boss said that Protocal gives you 1/4 information, because the person who wrote protocal asumes the readers have the left 3/4 knowlodge. that is to say you can 't depend on protocal esp when you do not have much background knowledge.