System is on a separate partition and the only way to free up space there is to delete system apps, which is probably not something you need to do unless you are running stock and want to remove the bloatware. System will naturally take up a certain amount of space just for the essentials. Those are the apps that are protected, as well as the OS itself. I wouldn't worry about freeing up space there or filling it up as you don't usually install anything in system anyways.
Edit: Just FYI, AFAIK the only two partitions that share the same memory space on this phone are the 'Internal' partition and the 'Sdcard' partition. Filling one of them up will also fill up the other because they 'share the same space'. Best thing to do is not use the internal Sdcard at all, and to link2sd the big and non-essential stuff like games and entertainment stuff.
