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 from your Manage page after you have submitted your application.
Please note: Your recommenders and counselor will also be able to complete their recommendations or School Report after you submit, as long as they are registered in your application. They will have until the teacher recommendations and School Report deadline to complete, and all materials submitted by this deadline will be considered in your application review.