There are several methods.
1) Beeswax on a stick
Pinch a pencil-eraser sized piece of beeswax off of a beeswax candle and mold it into an eraser shape. Work the wax until it's soft, and poke the end of a toothpick in it. Now, take your tube of glue (I like Gem-Tac) squeeze dots of glue onto the fabric where you want to put a stone. It helps to have opened the glue bottle by poking it with a thick saftey pin. If you just snip the tip off with scissors you will end up with too big a hole and the glue will sort of glop out. Anyway, I can do up to about 50 dots, but beginners should start with 5 or 10 and work upwards. Once you've placed the glue dots, touch the beeswax to the glass side of a rhinestone. This will pick up the stone. Now push the stone into a glue dot. Ideally you will have used enough glue so a small ring of it will just start to ooze out around the edge of the stone. The surface tension of the glue against the stone will pull it off the beeswax.
2) Glue on a toothpick
This works really well with E-6000. Squeeze out a dime-sized glob of E-6000 onto a piece of scrap cardboard. Using a toothpick, pick up a little glob of glue from the big glob. Now touch the toothpick to the metal side of a stone. The little glob of glue will pick the stone up. Now press press the stone, metal side down, into the fabric. Hold the stone down with another toothpick, a pair of tweezers, an orangewood stick, a bobby pin, or your finger. Slide the toothpick out from under the stone, leaving the stone and glue stuck to the fabric.
3) A method with tweezers
Pick up a stone with the tweezers, metal side up. Squeeze a dot of glue on the stone, then press the stone into the fabric.
There are other variations, it seems that everyone has their favorite way of doing it. I like going for the fastest way, which is the beeswax on a stick way for me. You kind of have to experiment to see what will give you the best and fastest results.