What is the best method to design an automation system?

Hello, Design of Automation system depend on many factors like (Number of system I/Os, type of process, distances and locations of field devices, type of field devices....etc)
1- According to complexity of system you will choose your controller(s) type
2- Choose your communication protocols according to amount of data, distances and protocols supported.
3- Calculate your I/Os and configure PLC I/O modules.
4- Choose your SCADA software or HMI and define its location.
5- Build your network topology according to system levels and locations.
Regards,

Additional to what ahmed said, if you want to upgrade the existing manual control system then it is mandatory to explore in detail the process of the manual system. So, at the first stage you already have the minimum requirements. Next, you identify what benefits you wil deliver to your customer by the automated system.. you can discuss this with your customer. After that, you already have all the requirements so you can start designing based on your budget, resources, etc.

your question is to be understood in many several ways, First if you mean the procedure it's normally a traditional one, which starts with arranging all the parameters of your process, so you can start designing after that but if your question is about the way of programing it depends on the PROCESS, COST, SAFETY...

System Design Automation A Method for Designing a Digital System as a Sequential Network System which is considered best for process industry .