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All of this can be very confusing and hard to understand. No one really learns all of it in order at once. Over time you will have aha moments of knowledge here and there that you will connect the dots over time.
Most of music theory doesnt even help to know. Does mario andretti need to know how pistons works in order to drive his car? No. But it is nice to learn.
The letters given to each note are nothing more than reference points to describe where the other notes in the song are in relation to the main note (the key or tonic note)
In the end scales are nothing more than preselected notes that simply sound good together. Play a scale wrong and you will instantly hear that you played the wrong note. The off scale note just doesnt jive with the other notes in the scale. Along time ago…Someone was smart enough to figure out what sounds good together and this was the best way to communicate it in a universal language regardless of instrument being played