I'm not sure I quite understand your question. I assume you don't want to grade the way your quizzes etc were given. One way could be to create grade categories 'Included' and 'Excluded' and push the non-graded assignments to 'Excluded' category. Then create a manual Grade Item using 'Add Grade Item' in the gradebook. Grade manually the way you want. You will need to define thru a formula the total for the 'Included' items to include the manually created item.
Not sure if this addresses your question.