The season two update has made this a little easier. Each map has up to 20 points of interest, listed in the top right of the map. When looking at the map while loading or by pressing up on the d pad once in the encounter, you will notice the POIs labeled with triangles. If the triangle is completely filled black, you have already discovered it. It it is unfilled, with some white, then you have not discovered it.
Just work your way around the map, each time you discover a new location a notification will display at the top of the screen. Once you have discovered them all, whether in a single encounter or many, the achievement will pop without the need to extract.
As for tips, I only have a few:
The triangles do not show elevation, so if you are right one without discovering it, look up for a bridge or upper floor, or down for a cave or tunnel entrance.
If it appears to be one structure at the triangle, you may need to enter the structure to discover it. If it appears to be a cluster of structures, then you probably need to be in the middle of the cluster to discover it.
Green symbols, such as the barred house, can cover the triangles. Either check them out or wait until the next encounter on the map.