I had the same issue when I started learning all this 7 years ago. I hacked my way though it until the lights came on and it all made sense. I have the process down to a (figurative) science, and have actually automated much of it and making 6 shade profiles can be done in 1 1/2 sheets of 8.5x11 paper.
I am in the middle of writing an updated a user guide, and should be done by the end of the summer. It is much easier when using a photospectromter, and creating ink limits and crossover points is not an arbitrary process.