Your achievements in science will definitely give you an advantage in the admissions process at the most selective colleges. You're not even a junior, and you've already won or placed in competitions at the local, state, and international levels. I think colleges will especially appreciate your demonstrated commitment to science, seeing as you've been competing since eighth grade and have consistently presented successful projects every year. This level of dedication indicates that you'll most likely continue to do important scientific research as a college student.
During the upcoming year, you can continue to build and improve on your (already amazing) achievements. If you were to earn a category placement award for ISEF, that would be the next step up in that competition. It's not a bad idea to shoot for that goal this year if you already plan on competing again. However, just being a two-time finalist is plenty impressive in itself. As he writes in this article detailing his successful Harvard application, even Allen Cheng himself was not internationally ranked in the ISEF competition. MIT will be especially interested in your ISEF track record.
If the rest of your stats (test scores and GPA) are on track with the expectations at the colleges you mention and you stay on this same course throughout junior year, you'll have a very strong application. You sound worried about how slightly different awards profiles will affect your chances, but I don't think you need to be considering the accomplishments you already have under your belt!