I'm new to trad too, but I've sorta figured out this dilemma. At least for me.
At longer ranges 25yds and out, I use the gap shooting method.
I too had the same problem you are having. I was pretty impressed with my 40yd shooting. It was easy, because my point on is right at 40yds.
When I was shooting 20yds and under, I was consistently shooting high, on center, but high...
I figured out the gap I needed to hold under at close ranges, but it didn't sit well with me.
I started focusing very hard on my target at "hunting" ranges. 20yds and under. Now, I'm to a point where I pretty much shoot instinctive at the closer ranges. I don't focus on the point of the arrow. I focus on where I want to hit on the target.
I've found that I mentally adjust at 10yds to hit where I want and out to 20yds.
I can't really describe it, it just happens now.??
All I can say, like the others have said too, just keep at it. It will all "click" eventually.
Good Luck,
BuckyT