Do I just chose what's more beneficial for my hand's flexibility or something?
I'm an absolute beginner attempting to teach myself how to read music notation.
Sorry if the headline question is confusing. let me elaborate with an example...

The bass clef staff tells me the first note of the song i'm learning starts with E....
I've noticed on the fret board, the second fret- A string, the natural note is E1. Alarmingly, the exact same natural note can be found on the 7th fret's E string....B1.
(Correct me if i'm wrong. I've been using 'Guitar Bass Notes' from the Play Store to gather this information.)
Long story short, would it matter which fret I finger for that beat? If so, how am I supposed to know which ones to choose. There's several of copies down the fret board. Ledger lined notes are easier to understand for they have a different music symbol to differentiate.