AMCAS does averages by credits. But first, they scale credits to some "standardized" credit. I had classes from a bunch of schools, including ones where a standard course was 1, 3, 4, or 12 credits. After their scaling, these were mostly 3 or 4 credits.
Most likely, your 3 credit classes will stay 3 credits and your 4 credit classes will stay 4. So you should probably just calculate your average by credits.