Lyn,
firstly a pic/photo always helps, assuming you are putting on a skillion roof? Or you are pitching a roof? The notching at the top plate is this the birdsmouth on the end of the rafter? Are trusses an option?
What span are you talking about and grade of timber? You can always use a different timber grade to reduce the rafter height, even use LVL's etc at a higher cost of course. More info needed.