For the longest time that always seemed like too much work for me and I'd use just one or the other. After a year if learning over and over that epoxy really doesn't stick to anything (at best, it's just a friction fit until it dries) and it's just about impossible to use enough superglue to fill the voids, I finally tried it that way. It works considerably better and isn't all that difficult, but you do have to work fast(ish) since you have multiple things drying.
I get everything set to go first. The epoxy is open, the superglue cap is loosened and checked to make sure the end isn't covered in dried glue, various tools and towels are next to me etc. I also make sure to choose a location first. If I'm leaving the stem on the plug, I'll often grab an empty plug first to make sure it'll fit properly. If I'm cutting off the stem or removing the plug altogether, I'll do that first and let [whatever is going to be in contact with glue] sit on a towel so it can get as dry as possible before I come back to it.
Next, pinch off some epoxy and start kneading it. After about 30 seconds, work it into the approximate shape you'll need it in. For me, I like it be kind of a teardrop shape with flat on the larger end. Grab the glue, but a big glob of glue on the plug and gently push the flat spot of the epoxy into it, hold it for a few seconds until it's dried enough that it's not going to fall off under it's own weight. Put a *big* glob of glue on the other end of the epoxy and shove it onto the rock. Use a bit of force too, you need to not only break the skin that forms on the superglue when it hits the water, but you also want the glue and epoxy to make as much contact with the rock as possible.
Sounds like a whole big production. But even if I'm just doing one, from the time I start to the time I'm drying off my arm is about 2 minutes.
It just takes a bit of practice. Also, knowing when something probably isn't going to stay put and moving it elsewhere as well as knowing if it falls, you can just fix it another day, it's generally not that big of a deal (though maybe at least make sure it's right side up when you notice it).