Hi there. I really think it's just a matter of personal preference for what form of progesterone to take. Although, I would think the suppositories might be best because they are right in the area where the progesterone is needed, if you know what I mean, but then again I'm in no way a medical expert! Anyway, I'm 7 wks pg and have low progesterone too, so my doc gave me the suppositories. I have been taking them a week now with no side effects yet--don't know if you've seen my other posts, but I have no real pregnancy symptoms yet at all. I will say that the suppositories are extremely messy--I've been wearing pantiliners all day since starting them because the medicine leaks out (sorry if TMI).
My opinion is if your doc thinks you need it, and you've already had two prior miscarriages, then go for it. If your body isn't making enough progesterone to sustain the pregnancy until the placenta is formed (around 10-12 weeks) then a miscarriage is almost a given. Two of my coworkers had problems conceiving, started taking progesterone before getting pregnant, and both have happy, healthy children. Good luck!