For good intonation, I play notes with the tips of my fingers, not the pads or the side of the fingers. I also practice 4 finger scales to get used to proper finger placement on the neck. I play open A, first finger, open A. Then place the first finger down and play 1st finger, 2nd finger, 1st finger. Next, place 2nd finger down, play 2nd finger, third finger, 2nd finger. The same with the 3rd finger and 4th fingers. Then go back down to the other way. I repeat the drill on all 4 strings in first position. This exercise helps me train my fingers to automatically hit the right note. I can make the notes in-tune by habit. I also practice arpeggios in first position. When I can play in tune, I speed up the tempo a little until I can play it in tune. These exercises help me learn how much space to put between the 1st and 2nd fingers and how close to put the 2nd and 3rd fingers. Hope this helps!