Best thing to do is to experiment. Play your songs, and listen to how they sound on the different pickups. To my ears, the neck sounds warmer, rounder, but lacks bite and definition. It's good for strumming when I want to blend into the background. Neck and middle adds a bit of Stratocaster quack to that sound, the centre has bite, but sounds thin. Middle and bridge tames the bridge a bit, and bridge is for maximum bite, maximum aggression, maximum articulation of all notes - for legato or tapping or pinch harmonics or punk or whatever.
Experiment, and maybe even make notes. I have an old piece of paper from my first: guitar - a hsh superstrat. I remember neck says 'BB King' , middle says 'Thin' etc.
Sometimes you want to break rules, too. Clapton's 'woman tone' for example, mixing neck and bridge, but backing off the tone on the bridge. Oh, that's another thing: each pickup with various tone knob settings.
For my live set, I know exactly which pickup I want at each bit, and have practice flicking the switch fast enough, so that I can launch into the solo on the bridge, coming out of the quieter bit where I am in between.
An hss strat is probably the most versatile of all guitars, so experiment. What sounds good for powerchords? For blues - what is more soulful? What is more biting? What artists do different settings remind you of? Have fun. Get to know your strat.