One of the best ways to really understand the CAGED system is to take a progression you already know and play the whole thing using just one shape. I'm using the Let It Be, No Woman No Cry progression, C, G, A minor, F, and playing every chord with the D shape only.
The key is knowing where the root note of each chord lands on the B string, because that's where the D shape is anchored. Find the root, place the shape, and you've got the chord. It works all the way up and down the neck, and hearing the same progression voiced that high up the fretboard is a bit of an ear opener.
Once this clicks with one shape, try it with the others. That's when the whole system starts to make sense.
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