Can anyone enlighten me as to how the substitute system works for this game?

Do I only get their points if one of my 11 doesn't play (as like most other squad based fantasy games)?

Or do I get their points regardless?

Or do they get less points than my starting 11?

You get points for the starting XI as well as for the 3 subs.

Doesn't matter if one of the XI (or the 3 subs) don't play in the real world - just means that you won't get deducted one of your 38 'starts' for that position...

You'll have to make sure and use it twice on another weekend (i.e. once on Sat, once on Sun with a different player)

Nothing for the 6 left on the bench.

Does the sub system work on each scoring day or is it over a game week(end) or something like that?

I can see that subs unexpectedly playing on, say, both this Saturday and Sunday could start to eat into your position usage allocation.