You can use any of the 3 strings, as long as they are the correct notes. If you look at many open chords (G major is a good example), there is a lot of redundancy. Though you are strumming all 6 strings, there are only 3 notes in there. The G note is in there 3 times (6th string, 3rd string, and 1st string).

What I say "you always flat the 3rd", it is the 3rd note in the scale. For a A major chord, that note happens to be on the 2nd string.

To make a minor chord, you can't flatten any string, it has to be the string (or strings) that provide the 3rd of the scale.

I hope that makes sense. I hope I'm not confusing you.

I learned guitar through chord and scale shapes and learned some theory later on. So I like to translate theory into what it physically looks like on the fretboard. So when I want to make a minor chord, I look at the major chord shape, identify the 3rd, and know I have to move it down a fret to make it minor.