Here are some answers to your questions. Others may have a different opinion and post answers, too.
1. Yes, you can use machine quilting thread in the bobbin. It can be either the same color or different, depending on the look you are going for on the back of the quilt.
2. The walking foot has an arm, which attaches to the screw on the side holding the needle in place. The up and down motion of the screw and needle cause the feed dogs in the walking foot to move. These will always move forward as the needle goes up and down. You take the risk of breaking the walking foot, if you use it in reverse.
3. If you quilt the diagonal stitches across the quilt, you can just run them off the end of the quilt. These ends would be covered and secured by the binding. If you choose a different quilting style, which does not go to the edges of the quilt, you must bring the bobbin thread to the top and tie off the ends together. Then bury the knotted ends within the batting of the quilt, using a hand sewing needle.