I think the answer depends on the material you are using for the shock cord.
Since you wrote that you are starting your first LPR scratch-build, I am going to guess you won't be using tubular nylon for a shock cord. For LPR, you might start by looking at Chris Michielssen's blog. Model Rocket Building
I think the Estes Designer kit comes with rubber-band shock cords. These are serviceable, but not very durable. A granny knot will hold well enough.
There is a diversity of opinion about this, but I am partial to 1mm or 2mm round or oval elastic cord like THIS. I use a a Kevlar leader from the motor mount with a swivel at the other end (close enough to the top of the body tube that I can reach it, far enough down that the Kevlar won't zipper the tube) Then tie the elastic in a loop with a square knot. I use the same pass-through the loop attachment Estes recommends for parachutes. Makes replacement at a launch easier.
Thanks jlabrasca! I did not specify but, yes, I was referring to tying the rubber band shock cords that come in the Estes kits. Currently I just use a square knot, and I wanted to know if there was a more reliable knot (my old boy scout leaders would be ashamed of how much I've forgotten).
For low-power rockets I usually use a figure eight on a bight to put a loop on the end of the cord and then a lark's head or cow hitch to attach the cord to the nose cone. For high-power rockets I second the PML knot above, but I tape the free end to the standing part with electrical or blue tape to keep the knot from loosening.