You can get verified without your mcat score, so submit it whenever your application is complete. However, school will not look at your app till they get your mcat score, so no, they won't send you secondary till they receive your score. The point of submitting early is for you to get verified early, because it can take up to 6 weeks. Once your mcat score is in, schools will start reviewing your app and send you secondary application.
Yes, you can add only one school and submit when you don't know what your mcat score is yet to avoid wasting money. After you know what your score is, you can add more schools to your app depends on how good it is.
Send your transcripts after you have completed your Courses section on the app, so that they will match properly. It does not matter if you send in your transcript before or after submission.
This pretty much applies to both TMDSAS and AMCAS. However, for TMDSAS, you have to pay by mailing your check to them, so if you add more schools, you will have to mail an additional check, which can take some time. So keep that in mind. And only mail your check in after submitting your TMDSAS application. Also, send in your transcript to TMDSAS as soon as you could, because it takes them forever to mark it as "received," (2 weeks for me). It is a lot faster with AMCAS though.