Yeah both work. Basically the decision comes in on whether or not the NPC sheet could be disposable, and thus the mission data would just need a new NPC sheet printed to be used again, or if you want notes scribbled on the page where all the mission data is itself.
I'm okay with them at the back, principally because oft times, an NPC can appear in multiple scenes, so it doesn't make too much sense to anchor them to a scene. Also, I like having them on one sheet so when I do the Threat Level lookups, it's all on one page.
Plus, on the separate page, you just need to print out a few copies of that one NPC section and the rest is reusable with out having to worry about erasing notes, etc.