On your application, there should be a place to fill in when you took/ plan on taking your MCAT. If you plan on taking it again, just indicate when you plan on retaking it. If your current scores are what are keeping you out, the BMS admissions office will wait for your new scores before they make a decision. I think as long as you apply early, it'll be okay- you probably don't need to retake your MCAT for BMS; you need to retake it in case you need to apply elsewhere. Once you get in to BMS, you need to apply for CMS the following year, and a shiny new MCAT score will go onto your app then.
I don't know too much about MAMS (I think that's the one you mean). I looked into it last year, but the way I understand it, it doesn't have a good linkage to the medical school at Loyola, and I believe you need to take a glide year after the masters program. i.e. after you take MAMS, you get your grades in the spring and then apply for the following year. I don't want to talk too much smack about any postbacc/SMP program, but in my humble opinion, spending 40+ grand on a masters degree is pretty risky if the linkage is low. And I'm not sure how a MAMS degree will help you if you end up not making the cut. Similarly, a Master's in Biomedical Sciences may not do too much for you if you don't get in to CMS, but at least the chances are significantly higher that doing BMS will land you a seat in Chicago Med. SMPs are all no doubt a big investment and therefore big risk. You should do everything in your power to tip the odds in your favor. This means studying really, really hard, and getting into a program that has the highest chance of getting you where you want to be.
