As long as your hair is growing, there will be some root exposure - your hair will never dread right down tight to your scalp.

That said, the best way to get them in line is to add a little 'root rubbing' to your palmrolling routine. Take each individual dreadlock by it's base, making sure you aren't crossing hairs over from other sections. Rub the sections gently against your scalp in all different directions (don't hurt yourself!) Palmroll as usual, from newly knotty roots to tips.