I use a variation on the "looking at the cup" method. I set up to the ball in about the right position, and then I look at the hole while taking a couple of relaxed practice strokes a few inches above the ball. While taking these practice strokes, I adjust my alignment slightly as required to make my natural stroke follow my intended line. (I also look down at the ball as necessary to make sure I haven’t adjusted myself out of position relative to the ball) After I’ve got the line and the set up, I make a couple more practice strokes, now looking at the hole and the distance, concentrating only on speed. I really focus on the feeling of the stroke for the distance. Then I look at the ball, drop down and sole the putter behind the ball, lift up a tad so the putter is hanging just off the turf, and I try to make the real stroke with EXACTLY the same feel as the last practice stroke. No thoughts except the feel of the stroke.

IMO, once you’ve read the green and can "see" the putt, your brain will make the right stroke, if you let it.