All you actually have to do is hit it twice, and it saves them, and then you don't need to hit it anymore. Once saved, the settings autoload at the begining of the mission.
S'cippy's talking about the "original" use of scroll-lock, which is to be the hotkey to call up the fleet-control panel.
One press of scroll-lock, without pressing shift or control, turns on the bottom (controls) and side (fleet formation) functions of the fleet control panel, while leaving the upper MFD "free" for normal use.
As Squadron Commander uses fleets extensively, you might want access to the various controls. Things like forcing your wingmen to fly in formation, fire on your target, only fire when you click on a little red target button that corresponds to their ship, use ECM, etc. etc. Also, if you want to fly in say an Echelon formation (cheap PFs protecting your leader PF), or the line formation (so that each PF gets a shot on the target in an overrun), etc. etc.
By doing this via the scroll-lock button instead of the fleet controller button in the upper MFD, you get those panels without the list of ships in your fleet taking up the entire MFD...