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Because of the modulular approach to programming that is taken in STEP 7, you should also take a modular approach to your program design.
Divide the machine/process to be controlled in modular units that must be controlled. Each unit can generally be subdivided further into subunits. For each subunit you should define the devices or operations that must be controlled.
In STEP 7 allocate the Functions (FCs) or Function Blocks (FBs) that will manage the operations of each subunit. Ultimately you will need to call these blocks according to the processing requirements. For example if you are dealing mostly with discrete logic controlled in FCs, these FCs might all be called from organization block OB1.