This is a great guide that helped me when I was first learning re-entry in the DG. I even had printed it out, and it should be here somewhere on my desk. Anyways, its great and IMO a great contribution for those just starting to learn.
It may not be that youre doing anything wrong, but that every vessel has different aedodynamic characteristics, and so you will need to adjust this technique slightly, depending on the vessel.
AerobrakeMFD can be very useful, just make sure to keep the predicted impact point well ahead of the target initially, you can always change to normal flight and glide down from the upper atmosphere like a plane.
With a little practice, and some thinking, its not too hard to refine a technique. Hell, if i managed to get the hang of it, anyone can