I know that there is an option to send in AP Scores when applying for college, but do colleges see all the scores regardless? Do you submit them while applying or after? Also is there a way to only send in certain scores?
There is no need to submit AP scores unless you think they will help your application. You do not need to send a formal report until after you are enrolled in a school. AP scores are self reported. There may be exceptions that others will know.
When you apply, you can self-report any AP scores you want the colleges to see, simply by entering that data in the application. You can choose to report some or none.
When you take senior year AP exams, you send an official report with all your scores to the college where you will already have enrolled.