Hi Ed,
You ask very good questions. My response by necessity will be subjective because if you look at originals, the layouts vary a lot, and that also includes brass patchboxes. You will see some on which the end of the box was more or less centered on the buttplate and the axis of the lid is perpendicular to the buttplate regardless of the shape of the buttstock. Often those seem a little off center with respect to the shape of the buttstock. I tend, when possible, to try and center the lid within the lines of the buttstock. I do that by drawing 3 lines, one for the top of the comb, one for the bottom of the stock, and one for the axis of the lid. Generally, I want the lines to converge about where the pan is on the lock and the end of the line for the lid centered in the buttplate as closely as possible. However, all of that requires tweaking depending on the shape of the stock, drop, LOP, etc.
dave