hey i have a kind of noobish question, but im new to this so please dont be too harsh. if you were writing a song, say, melody first, and you came up with that, how do you figure out the correct chords to go behind it (or vice-versa)? this has always confused me, or vice-versa. matching them up is hard. please help me
figure out what key its in first off, using the notes given.

then go for whatever your little heart desires. the key gives you an estimation of chords that you can use, but doesnt limit it. and as for progressions, its all about how you want it to sound.
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The answer to your question is scales. Learn your major scales, I used to circle of fifths for this. Then learn your relative minor, (there is an extremely easy way to learn your parallel minor that pretty much negates the need for memorizing them).

Eventually you will learn to match up chords and notes with scales and writing will become a lot easier.
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Theory is descriptive, not prescriptive.

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theory states 1+1=2 sometimes in music 1+1=3.
i get major scale chords, like I ii iii IV, etc. "should" (i know there are no rules in music, just guidelines) the chord being played contain the note played at the same time? for example if the chords went G, and then to D, when the chord changes to D, should I be playing the 1st, third, or fifth of a d major chord ( i dont know them off the top of my head)? sorry if thats a bit confusing im bad at communicating my thoughts through words sometimes
Harmony my friend....

Learn intervals, and study them and figure out how they sound and how they please you/etc..If you want a certain harmony, try using intervals you know will sound good/appropiate to the melody. Maybe even try learning counterpoint and how to use it too...

This is the basic thing, like if you were writting a classical guitar song, but if you only want to play backing chords, learng diatonic harmony (major/minor) and how chord progressions work/cadences/etc.
If you want to go further, learn chord extensions and how they apply to each interval, etc..

Frankly, I don't know much about it either but well...