I oversew them by hand first. Then machine sew them with the pad on top. I'll also make marks (little dots) right round a quarter of an inch in to remind me of the seam allowance. When I get to a seam, I stop, left the machine foot, check nothing's trapped, then carry on. I also tend to do this bit really slowly, sometimes even turn the machine by hand rather than use electricity so I can control it.
If I'm using leather, I handsew with a glover's needle.