Stop!
There are alternatives to Mr. Jacobson's method that you may wish to consider.
Measuring down from the top of the stem isn't helpful-- rather, use the proper waterlines as a guide. Don't leave a loop of rope dangling out of this hole-- tie into it when you need to on the river. The DWL (Design Water Line) as a place to start-- one shouldn't load the boat above this value, so consider putting your lining tube somewhere near it-- say 2 inches above.
The DWL (and all waterlines) are measured from the bottom of the hull and up toward the sheer line. You'll have to level the boat on the floor and measure up from the floor to locate the DWL as given by the manufacturer or designer.
As Mr. Jacobson said, start with a tiny drill bit, but use a Forstner bit to drill the hole. Composite-cutting Forstners may be had, but they're expensive; so get a brand-new regular Forstner of the appropriate size from Home Depot. It will cut your composite (or Royalex) hull beautifully. Go slow and gently rock the bit from side to side as you cut through. Toward the end, tip the bit some and let one side begin to break through first-- don't burst through flat!
Clean up the hole with some 320 emery cloth wrapped around a 1/4" dowel (a rat-tail file is too coarse, and will chip out the gel coat).
If your boat is composite, seal the edges of the hole with some epoxy and let the fibers drink all they want. Something like Kevlar is fairly hydroscopic, and that's why the fibre edges need to be sealed. While the epoxy is still green, glue in your PVC tube (rough it up with 80 grit). To prevent the epoxy from running, thicken it with silica.
After it's all cured, trim and finish as Mr. Jacobson suggests.