...you'll want to not be quite as liberal with the glue at the edges of your shapes—both for tacking down the seam allowances and for adhering the completed shape to the background fabric. Do your best to keep the any glue out of the fold of the applique shape where your needle pierces the fabric.
A sewing machine has no problem stitching through the glue.
However, with a hand needle, YOU are providing the 'force' and I think it would get tiring to push the needle through the amount of Elmer's Glue stick that I use.
Try a couple of practice pieces first to figure out how just how 'little' glue stick YOU need. I'd make a couple of shapes with curves and inside and outside points to cover all possibilities.