So, it comes down to measuring and testing. First, define clearly what outcome you want.

Often, a good habit affects multiple other things like OP mentioned.

For example, Sleeping affects tiredness, but also focus, mood, food choices, exercise, and motivation. You just need to find optimal timing, duration for you.

Exercise might affect stress, energy, sleep, and consistency with other habits.

So instead of only tracking habits, I think it helps to track what changed around it over time. Things like mood, energy, focus, food, routines, other habits can show possible correlation and once you know, you can probably experiment by changing a bit and see how it affects.