Gorgeous quilt Iminei! There are as many ways of applying rhinestones with glue as there are people doing it. Whatever method you end up using, try to avoid having a stone cross a seam junction if you possibly can; the stones will adhere better if they have a consistent surface to take the glue. If you're using Gem Tac, I'd make sure the quilt is flat on the table, not hanging, and can stay flat and undisturbed until the glue has cured. This can take 24 hours or more, depending on the weather.
What size rhinestones are you planning to use? How I apply the glue depends often on the size of the stone I'm using. For larger ones (over 20ss), I tend to use the Gem Tac bottle with a very small hole in the lid, to place a small dob of glue (about the size of the stone you're using) directly onto the quilt where you want the stone. After the glue has had a chance to go "off" a little, I use forceps to pick the stone up and simply place it on the glue.
If the stones are smaller, I pour a small amount of Gem Tac onto a square of silicon baking paper or a small disposable plastic plate, then I use a toothpick with a dob of orthodontist wax (or worn out Blu Tac) on the end to pick up the stone, shiny side up. I dab the flat side into the glue, making sure the entire flat side is coated in glue, then I put the stone glue side down where it needs to be. If needed, I use forceps to gently disengage the stone from the toothpick.