Yes. You should submit your application even if other materials are still outstanding. You will be able to upload your transcript, test scores, or School Profile through the Upload Materials section on your Manage page after you have submitted your application.
Note: Your recommenders and counselor will also be able to submit their recommendations or School Report after you submit your application, as long as they are registered in your application. They will have until the deadline to submit, and all materials submitted by the deadline will be considered in your application review.
You can and should submit your application once you are ready even if your recommendations or School Report have not yet been received.