I know those circles in the circuits mean 'Not' ... Every time I see a circle do I need to flip the values?How does it work?
Like said before, yes, and be aware of timing too.
You can see those circles in places where you think they are
not necessary, and that can have multiple reasons.
For example: Sometimes a signal has to amplified/buffered/limited/filtered, and an easy way is/canbe to use an unused NAND port that is present anyway.
But now the signal is inverted? No worry, that's easily solved in software or port settings.