If you put the glue only in the seam allowance and then press to one side or the other it wont matter about the glue. If you are trying to press the seams open you will have to pull them apart after the seams are sewn and before you press the seams.
I use a dot of glue in the seam allowance, set it with the iron, sew the seam, and press to one side I don't have to mess with pulling the seam apart and you don't even notice the glue is there after the seam is sewn. I like glue over pins because I have small kids and cats, if I pin a project together and then don't get to sew it right then and there someone (or something) is bound to pull a pin out! The glue allowes me to match seams now and sew later without the worry!