It's easier to sew a wider seam, half inch or 5/8" in heavier fabric. Often, the instructions will tell you to 'grade' the seam after sewing. Usually you cut one layer down to about a quarter inch and the other layer of fabric a bit wider. This reduces bulk and makes the seam lay flatter. Cutting the entire seam down is less usual, but again it's difficult to sew a narrow seam in heavier fabric or a bunch of layers. Here's a youtube video on grading seam allowances:
http://www.youtube.com/watch?v=_gseV1cF9o4