In order to make your own protocol for molecular biology, you have to read lots of research article that correlate with your study. Then, you select the best protocol that suits your study in term of availability, budget, and reliability. After that, you try to run a pilot study based on the protocol, and optimize the protocol until it suits with your study. And the final protocol is your own protocol.
I completely agree with Wai.Standardising protocols is the bread and butter of any researcher. Protocols that we use now is the result of enormous efforts of numerous researchers. So, to make your own protocols, you must first know and understand the already existing, standardised protocols and how they work. Having a clear idea about the mechanism involved gives you the edge for developing better protocols for your own purposes. According to your needs then you can modify it to see which modifications give you best possible result in a trial and error method.