This was my thinking on the matter -
I had taken all the prereqs while in college, except for A&P and an Adult Development psych course. I had also taken chem, bio, and calc through multivariate calculus (so, AP Calc in high school and then a couple of advanced semesters in college.) Had I done very well on those science and math classes, I would have applied last fall (2010) and then taken my prereqs (which are now done) this past year, and (fingers-crossed) started an OT masters program THIS fall (2011.)
But, despite doing 4 years each of every major subject in high school, at honors or AP level, and getting into an extremely selective college, I then totally screwed around my freshman year and didn't do well in those college science and math classes. So, I felt like I really needed A&P DONE with good grades before I could apply at all - basically, I really needed to show that I can do well in science courses. So, this past year, I took A&P I/II w/lab, and Adult Development, at the Harvard Extension School, got A's in each course, and feel much more confident about my application chances.
Some have said that in certain regions, even though the schools will say that you can apply with your prereqs in progress, you'll really be at a huge disadvantage. Who knows how true that is in every case. But you should look at YOUR case and see if you think that your application would be stronger with good grades in A&P. For someone who was, say, a chem major or a bio major or a physics major with a good GPA, A's in A&P might not do much more to make the case that the person is good at science. But if you don't have much in the way of science classes in your background, or you didn't do well in those classes, then you probably want your prereqs DONE before you apply. Or, I suppose you could apply and see what happens, but I don't know whether having to apply a second time if you don't get in the first time would reflect badly on you. Waiting a year can be frustrating - I have one other masters and am changing careers and quit my job a year ago to take my prereqs, making this a LONG process - but it could be worth it.
My two cents....
Oh, also OP - don't you need two semesters of A&P so that even by December you wouldn't have all of your grades for the schools to consider? Also - just double-check (if you haven't already done so) with the schools to which you're applying since not all schools allow prereqs to be in progress while you're applying. Most I've seen do, but some don't.