This is the way I have seen it work and understand it. Keep in mind that since all of the STA-21 stuff has gone into effect, this information could be totally wrong. Marines who have been enlisted for some time, and have achieved the rank of LCPL, can apply to the MECEP program. I'm sure there are some tests that are a part of the application process, such as taking the SAT, etc. Some marines who are accepted are allowed to report straght to an NROTC unit after attending MECEP prep school which is a few weeks long. Others, who may be found needing an academic "BOOST", (no pun intended, will be allowed to attend BOOST in Newport. Kinda works the same as an NROTC scholarship where some students are allowed to go straight to college while others will attend BOOST for a year before going to college. This is the way it has worked for the MECEPers who are at my battalion now and those that have recently graduated. So in short, only applying for MECEP will get you into either option, I don't believe Marines apply directly for BOOST.
Hope this helps, ENS Ray (newly commissioned, woohoo!!)