I make all of my templates without the seam allowance.. I'm a hand stitcher.. that way I mark the stitching line, then add 1/4" and have a cutting line...
Easiest way to add seam allowance is to take 1/4" ruler and make a series of dots around the perimeter of the circle, then join them together. you can do this on a sheet of plastic template material and have a new template, seam allowance and all. You can also buy a "flexible" 1/4" strip at LQS for this.