The "system" isnt just the software. The system might include aspects of the environment where the software works. Say, If you have a software for managing a depot, your system might not only be the piece of software you have to develop, but also the bigger system, the entire depot, who might depend on other systems, say, administrative sector, maybe there is another piece of software for sales that needs to interact with the depot's software, or even maybe a non-software part, like the dudes who work in there and do specific tasks that the depot system has to control.
A part of Software Engineering is system's engineering and system analysis. Which deals with how to tackle these kind of things. There is also project management, like deciding on what development technique fits best with the software you have to develop, do you need a non-functional prototype working in two weeks to get the client's feedback on it? Or you can present it on a few months with some functional parts already implemented? How many people you got? Have they worked on a similar project before? If its the case, can you reuse some of that code on this project? Does the client has the hardware needed to run the software you're developing? And a big etc.
Its a big topic, and entire degrees based around it, and all of them can teach it from different perspectives.