Wow. There are at least three or four ways to do it, and everybody has a favorite. Mine is to use an integer register to hold the "Step" and move from 10 to 20 to 30... etc. I've also used bits but you have to hold those on (or use latches) and it's harder to insert new steps if you've used bits in the original sequence. On the other hand, bits process faster.
I generally number by 10's; this lets you set up some numbers between steps as process faults (i.e., the process step is from 10 to 20, but 11 might be used to indicate a particular failure of the 10 to 20 transition) and also leaves room to insert rungs later. To formalize it a little more, Steps 10 to 99 are used for start-up logic; Steps 100 - 199 are used to test interlocks and initial conditions before running the sub; and 200 - 899 are for the normal subroutine logic. If a subr is on Step 899, then it's done and waiting for it's next cycle; if it's in between, the subr is running; and if it hangs up, you look at the Step value and immediately know where and why.
The beauty of using state logic for a sequential machine is that you can program for fault recovery, safety and maintenance all at the same time. If the machine stops, you know why and you can write logic to recover from fault conditions that all can have numbers! The machine is safer because actuators don't fire just because somebody broke the beam or made the switch; the sensor is processed only on the step that needs it, and the rest of the time it's ignored. And, as has been said, state logic is easy to read and follow since it moves one step at a time through a sequence, and you can follow those steps.
There is no "best" way to do it, and in a real machine there are a lot of other things to worry about like actuator and sensor fault handling, parallel and series processes, subroutine and machine reset and initialization, minimum cycle time and data development and collection. And every time I write a sequence, I learn something else about how to do it better. You have the idea; try laying your steps out using bits or numbers and see what it looks like.