Steve,
After you get the basics down, the Andys Shot Glass article is great, then check your seconary alignment in the normal manner. Instead of the paper ring on the mirror that most have now for using a laser, make a square of something black. I use plain old electrical tape, with a hole in the center to reflect a laser beam in case I ever use one. With my cheshire a square about 5/16 to 3/8 is about right. You want a square the size of the black occluded spot of the cheshire. When properly collimated you will see the 4 tiny corners of the square sticking out of the cheshire spot. A triangle works too, you just need those tiny points to know when you are perfectly aligned.
After you think you are collimated, you can reach in the top of the tube and gently twist the secondary to and fro, you'll see the black square move in and out of center of the cheshire spot. I have an old junky, and also pretty dirty, 6X30 finder I stick on the cheshire and can see a really magnified image, I can dial the secondary in just about as close as I can get it with the auto collimator.