Here's my advice, for whatever it's worth:
If the summer courses will really bring up your GPA significantly (from a 3.3 to a 3.5 or something dramatic like that), and your current GPA is low (under a 3.5? I don't know what you consider low), then it's not a bad idea. However, since you're applying to medical school this year, I'm assuming that you're a junior. Given that, you probably have 90+ credits already, so that 3 or even 6 additional credits won't really make a difference in your GPA. The only exception to this, in my opinion, is if your science gpa is low and you've only taken a few science courses (just pre-reqs, maybe one or two more) and the classes you are planning on taking over the summer are science classes that you think you can get As in. Then it might be worth it.
Otherwise, I would say just send your transcript in now. Some people have told me that schools often request grade updates with your secondaries, so you can always send your summer scores then. Also, i'm pretty sure (but ask a pre-med advisor) that once you've completed your AMCAS file, you can still ask them to update your grades and have your school send your updated transcript.
If it were me, I would send everything in as early as possible; I know that in a lot of places, sending things in early is huge plus, especially if you feel that your stats are borderline.
Well, that's my two cents. Good luck 🙂
- Zina