The answer to your first question … which may sound like something of a cop-out … is “a little of each.”
Admission officials will certainly realize that your son’s strengths are skewed. But if they feel that his gifts (both academic and extracurricular) outweigh his deficiencies, they will admit him. If, however, the admission folks see his strengths as being comparable to those of “competitor” applicants who are firing on all cylinders and feel that there is nothing else about his credentials that jumps off the page, then his news may not be good.
Several years ago I worked with a student who was, like your son, outstanding in math and science and much weaker in English and writing. His acceptance list was all over the map. For instance, Middlebury, Wesleyan, and U. of Chicago (among others) all admitted himbut Amherst, Carnegie Mellon, and Haverford did not.
However, many engineering programs will put the greatest emphasis on the math/science. This boy cited above was not applying to engineering majors so his English Achilles Heel may have hurt him more than your own son will be hurt at engineering colleges.
Because college officials will not see your son’s AP results until after admission verdicts have been issued, you should certainly encourage him to take math and science SAT Subject Tests to show off his strong suits.
Your second question is much easier to answer. Colleges will definitely look at senior grades and these grades can be more important than students (and their parents) often think.