We have a just turned one Red Setter. She is a very good family dog and we are very happy with her. We have watched have the Puppy Dvd and the Basic Obedience dvd, both were extremely helpful. She knows her commands and performs them when asked. However, she is not the brightest dog in the world. She has a lot of energy and a very short memory. We knew that before we got her and like her inspite of it. She is not allowed to be loose in the house without supervision. She has been corrected 99% of the time she jumps up on the furniture, goes up stairs to the bedrooms, tries to eat off the table, and scratching at the sliding glass door to go in or out. These are her big offences.

We are obviously not very good dog trainers. When I correct her with a very sharp scruff shake and a determined NO, she cowers. She even knows it is coming, but she seems to be totally ruled by her id. She can't help herself. She is trained on an invisible fence. Would an e-collar help with this behaviour? The scratching at the outside of the door is the one that has us most perplexed. She has just figured out she can bark, so perhaps there is a way to get her to bark to come in rather than scratch.

Any advice would be appreciated.

If you are asking how to teach the dog to bark to come in the house, I guess you would start by teaching speak. But maybe you could look at it this way. when you let a dog outside it does not get to choose when it gets to come back in. You do.
As far as the cowering after the correction, I am assuming that it means nothing and that she will get the food off the counter again, 1. check the timing of the correction. You have to catch them as they are doing it, not after. 2. Knowing that you have a dog that does what it wants whenever it wants, if you are not watching it put it in it's crate.