The most important part of any automation job is to define what you want to do -- start with a description of your process. I would guess your process could be described very well by a flow-chart.
Define your I/O (not PLC addresses, but the required devices - sensors, actuators, etc.)
Define each step in the process.
Define the transition from each step into the next step.
Define system faults.
Define how a fault condition should be handled.
Define how the operator interacts with the system (start, stop, alarms, etc.)
etc. etc. etc.
Do this BEFORE you ever even start thinking about writing code!!