if it better to follow c, d , e, e# etc… or c, g, a?
Think of music theory like learning a new language; there is no objectively "better" pattern of words to create a sentence. It depends what you want to say. Of course you need to learn basic rules to start, like IV>V>I or ii>V>I chord progressions, but that won't take you very far. After that there's a near infinite musical vocabulary you can use to make interesting music.
Primarily, keep listening to, learning, and analyzing music you love. That is the most natural and fun way learn, but it also requires a baseline of music theory. For that you may want to supplement with some academic reading such as these:
more guitar oriented:
https://www.amazon.com/GT15-Guitar-Grimoire-Progressions-Improvisation/dp/0825831970
more general which will require some musical notation reading:
https://www.amazon.com/Chord-Progressions-Theory-Practice-Everything/dp/0739070568