Ahoy...
My understanding of them, is.. unlike SH4's mission area designation... you're not tied down to a set area defined by a circle & having to stay inside it, to complete the mission objective...
Which, I have to say is nice. It harkens back to SH3 where you get told ok, patrol say... AM18, you go there & patrol in that zone area... any portion of it, not just 1 particular portion of it... & after some time, you're done.
As I say, this is My understanding on it... I go to the general area & start roaming around & hit anything that crosses my path, making sure of course, that what I attack, ISN'T considered 'neutral'...
Hope this helps...
M. M.