This paper is focused on one of the majors problems that a designer, of an automation system controller, must solve that is related with the correct synchronization between different parts of the controller specification when this specification obeys at a previous defined structure. If this synchronization is not done according some rules, and taking some aspects in consideration, some dependability aspects, concerning the desired behavior for the system, may not be accomplished. More specifically, it is shown, in the paper, a systematized approach that consists, first, in using the GEMMA and the SFC formalisms for the structure and specification of all the system behavior, considering all the stop states and functioning modes of the system and respective synchronization, showed in detail. Secondly, using formal verification as analysis technique, it is guaranteed that a dependable specification has been obtained. A case study is presented to explain the proposed systematic approach.