What is the best resource for learning chromatography? This is independent of the equipment you use. Chromatography theory applies to HPLC, flash chromatography, supercritical chromatography, solid phase extraction, and even to liquid-liquid chromatography. Books such as Practical HPLC Method Development by Snyder, Kirkland, and Glajch are helpful. The theory applies to any chromatography system.
The second part is "How can I best run my Shimadzu system?" and "How do I create the gradient method I learned in question 1 above in my Shimadzu HPLC"? The manufacturer is the best place for these questions, their manuals and materials.
There are many books available however best practice books which is referred by pharmaceutical industries is Open learning book and Fundamentals of analytical Chemistry by Douglas A skoog.