I'm in the process of creating a new diet plan with http://www.eatthismuch.com/ however I'm unsure with workout days if I should be intentionally eating less calories to account for the ones I'm consuming with my post-workout protein shake. How do people normally do this? Do they discount the shake or do they simply adjust their meal plans accordingly to account for it?
A shake is food; you're eating it. If you're trying to maintain a certain daily calorie level (e.g., maintain a specific deficit for weight loss, or surplus for gain) then both the shake and exercise must be counted.