Actually, I don't do it at all; I'm making my first recirc skimmer (I've made many beckett skimmers) and I'm putting a small box underneath the tube so that all the plumbing goes through it. But, I have made many holes in tube for waste drains in collection cups. The way I do it is I find a PVC fitting that has an I.D. the size of the hole I want, then I tape some coarse sandpaper to the inside of the tube and sand down the end of the fitting so it matches the curve of the tube. Then, I remove the sandpaper, mark where I want the hole, and drill a 1/4" pilot hole. Then I use double sided tape to attach the fitting inside the tube where I want it and use a flushtrim bit to rout around the inside of the fitting. I usually keep a hand on the fitting inside to make sure it doesn't go anywhere; if it came off that would really suck. But using the router makes the hole turn out perfect. I do get a little tape on the bit when I do this, but it's easy to clean it off. Of course, you could just use a drill press and the right size plastic bit, maybe a couple of wood stops and a clamp or two to hold the tube in place. For me the router method works great, and once you have a PVC fitting sanded to match the inside curve of the tube to use as a template, it's really quick to make holes that size.
