The questions are mixed together. Sometimes you might not know which test the question is for because the information can overlap, but most of the time you can probably guess if it's a genetics question or a biochemistry question, for example. It's annoying if you're the type of person who tries to guess what you'll score based on how many questions you think you got wrong, but otherwise I didn't find it to be a big deal at all. Also, it's not like the answer choices are mixed around, so you don't really have to worry about which class the question is for. It's worth noting that these exams, while long, aren't really time pressured. I think I finished most of the four hour exams in around 3 or 3.5 hours at the latest.
Don't prepare for the program over the summer! Relax. Seriously. Besides, you don't get the syllabi (like the class textbook), or access to the lectures or anything until the beginning of the year. Maybe do some reflecting on why you ended up in the program in the first place - was it your study strategies in undergrad? time management? distractions? I think self-awareness is important for being successful in the program. If something isn't working for you, change it (be it study location, study strategy, friend group, whatever). If you don't understand something, ASK FOR HELP. The professors, TAs, and even classmates are happy to help you. Pace yourself - don't go so overboard with the studying that it's unhealthy, but try not to fall behind on the lectures. If you're going to skip a class, watch the lecture in the next day or two so you don't fall behind. Make friends. You need people around you to vent about how stressful everything is. Having a study group is also really helpful for the spring classes, so try to join one. If yours stops meeting, ask to join another one. Even if you don't like working in groups, at least give it a shot. It's good to have friends who can keep you accountable, who can share study materials/strategies, and who can help you out if you don't understand something. You got into this program, you're smart, you can do it, but you have to be willing to work hard, and be flexible. Don't freak out if you get one bad test score, it's one of MANY exams, just don't make it a habit. Try to meet with your advisor multiple times throughout the year so they can get to know you. Again, if you're struggling with anything ask for help, especially from the TAs - they've already done this program and they know how to do well.
And back to the summer thing - honestly, just enjoy the free time you have. If your application could use more clinical time, think about volunteering or working. Consider taking the MCAT if you haven't already, because the MCAT class schedule in MBS is pretty crazy. Other than that, just hang out.