That's one way of doing it, actually. I tend to glue my SPS frags (and some LPS) directly to the rockwork. Some people mount them on plugs or discs to make them easier to move around.
For direct mounting:
Generally I take a small amount of glue to the bottom, then dip it into the water to solidify. This helps protect the bottom of the coral and lets me add more glue to it without getting it on the frag. If it's a big piece and will need a lot of glue, I'll do this a few times to build a base. Once I have it the size I want, I add enough glue to cover the base and get it to stick, dip it in the water for a few seconds then take it out for a few. (You don't need to do this, but I find it helps make the glue a little tacky so you don't have to hold the frag for 5 minutes waiting for the glue to set.) After a few seconds, I attach the frag to the rock and hold it for 15-30 seconds.
In a healthy tank, it will usually cover the glue pretty quickly and look very natural.