I need to know one thing and I'm getting really confused about it. I'm in C major scale and there's an E minor which the forumla is 1b35 right? So wouldn't that mean a bE(3) rather than a natural E

E minor triad is E G B.
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In the key of C, you have chords for each note.

I ii iii IV V vi viio

smaller roman numericals mean minor chords. This is only in a major key.

E is minor. Major E is E-G#-B. The minor is E-G-B
1 m3 5

Minor 3rd = 3 1/2-steps (frets)

So count up pen E at zero fret to 3rd Fret (G).

Does that make it any clearer?
Ah, yes I'm a fool.. it all makes alot of sense now. Cheers.
for Em, you start the count at E.

1 3b 5 from C would give you a Cm.
In C you have an E minor chord. Not an "E" which is a minor 3rd in the key of C. I think that's what you were getting at, right?
I don't think you have an understanding of some of the basics yet. Do some reading on musictheory.net and also search for the Crusade series. That shoudl get you started.
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Big deal, I bought a hamster once and they put that in a box...doesn't make it a scale.