I handpiece all of the time and you have to plan ahead a little. What I do is mark my 1/4" seam with a fine mechanical pencil. Then I make a tiny mark at each corner 1/4" in from the edge. Then when I hand piece I insert my knotted thread a 1/16" of an inch or so before the 1/4" from the edge mark. Then I stitch backwards to the edge, and backstitch back to the mark. Then I stitch the seam and backstitch at the 1/4" mark on the other end, stitch to the end, backstitch, and finish a little over the mark. It's hard to explain, but I never have a problem with cutting my stitches and having the pieces compromised. I always trim to square.
I find that marking your seam allowances is very important. I haven't had a problem using a light pencil mark. I also square as I piece so I rarely have issues with unmatched points.