Yup, the schools will usually only see that first semester, but the Deans of your school will usually send out an update letter before the semester ends indicating your performance on some of the earlier tests. Some programs use the block schedule instead of semesters, so technically, you could have completed an entire course before the end of a normal Fall semester.
You'll notice some SMPs put the "more important" courses first, and also some easier ones to help boost your scores. This way, you look good from the start. But, you'll need to perform well throughout the entire program if you'll be applying the next year, since med schools will see everything. Also, some schools give guaranteed interviews to the top certain % of ppl in the program, and they'll wait to see more grades through the spring.