The way I do it is I just apply it directly from the bottle, remember this stuff dries quickly so any other method would probably just be messy. Make sure you do it when your nipple is contracted and in its smallest form like after a cold shower or something. I actually found that putting on a very thin layer of the glue looks very natural, and I like to only put on enough to cover the nipple not so much the area surrounding the nipple. The only way someone would notice it is if you've had it on for a long time and it starts to crack, which doesn't happen for a long time if applied correctly. When touched it is not sticky at all, in fact it is hard and dry, but as long as no one rubs your nipples I doubt anyone will notice it's even on. The tricky part is getting it off. It does not wash off easily therefore you have to peel it off, the longer you leave it on the easier it is to peel off, but peeling it off can be a little painful as the skin on your nipple is very sensitive. Even after wearing a shirt all day and showering after the gym the stuff stays on, and I'm guessing if you didn't remove it yourself it would stay on in excess of 12 hours or so. I personally put it on before I go out somewhere then remove it every night before I go to bed, I haven't actually done a longevity test to see how long it stays on.
A couple other tips:
After the glue has dried do not play with it, doing so will only cause it to peel faster.
Trimming the hairs around your nipple will make peeling the glue a much less painful process.
Try not to peel and reapply too much, the skin on your nipple is too sensitive to handle it.
Anyways I've been using super glue on my nips for a while and it's quite astounding how natural it looks and how well it holds. If I did this every day for the rest of my life no one would ever know I had a problem with puffy nipples, but this is only a temporary solution, probably the next best thing to surgery though. If I find a better way to remove this stuff I'll let you know, but I strongly suggest giving the super glue idea a try as it's worked wonders for me since I started doing it.