The knots themselves should be tight, but not the part of the thread inside the quilt. Think about buttons -- you have secure stitching, but there is a shank, so that there is some space between the button and the garment for the other part of the garment with the buttonhole to slip in between. It is the thick batting that requires special treatment. Try putting a thin piece like a small pencil, chopstick, or dowel between the quilt top and the knot. Tie tightly against the stick, so that the knot is secure, and then remove the stick. See how that works and adjust the thickness of the stick if the result is still too puffy or is too loose. I think the distance between your ties is fine, but the directions on the batting will tell you how close they should be.
Dayle