There are many ways to implement a program and I'm sure many here will come up with many different ways of doing it.
I have attached a pdf with a sample I think may help you it's a step sequence based on your filler, this is only a guide and I'm sure many others will say no you do it like this lol, anyway the program was written in GX works ladder as it probably is quite close to your sim program. The basic idea (as I don't think the info you gave us really gives all the information for example how do you start the process, although you have an output for conveyor 1 how do you start it it's not clear in you description. The program uses step Bits (memory bits/flags whatever you call them) and I have added some timers (long times) as this allows you to follow simulation, on actual program these timers would either be very small or none at all. The step bits are kept on until the end & the outputs are turned back off when required by the following step flags, the step flags are reset at the end of the sequence. Hope this will get you started.