It's a very personal preference. We have shaker cabinets and wanted bin pulls. We placed the pulls on the top rail of the drawers (but in the center of our top drawers, which are slab only) and the two pullouts. Our knobs are on the uppers. I've also seen bin pulls placed in the center of the flat panel on Shaker drawers with rails, which also looks nice, but our drawers and the pull size we chose didn't work for that configuration.
One thing I do like about having the pulls on the top rail of drawers is that it seems a more natural place to grab for the bottom, largest drawers.
We found it helpful to go onto Houzz.com and search for the pull style we liked and see examples of the different placement.

Dang, I had written a long answer yesterday, but must not have hit "submit" after preview.

First of all, it turns out that nearly any placement (within reason) will look fine. You can look through many houzz pictures to verify this.

What I did for the drawer stacks, which I got from someone here, was to center the pull on the top, shallow drawer. Then on the lower, deeper drawers, I placed the pull the same distance from the top of the drawer as on the top drawer. (A small advantage of this is that you need only to make one template!)

For the uppers and the cabinets, I just held the pull up to the door and figured out where I thought it looked "nice." Then I measured and standardized that. I wound up placing the pull so that its bottom hole was about 1.5 Shaker-rail-widths from the bottom of the cabinet door.

Thank you! Meeting w the cabinet guy today. I'll let you know how it comes together.