To use the binoculars, you hit Up on the D-pad. To tag an enemy, you must hold the box in the middle of the screen over an enemy for a little bit.
When you first place the box over an enemy, the enemy will be highlighted in white. If you continue to hold it over them (about 3 seconds), that highlight will change to green. At this point, the enemy is considered to be tagged. The highlighting will persist even if you move the binoculars off of them and they will be marked on the map and minimap. Note that if you get too close to an enemy, they will automatically be spotted by proximity. They can still be spotted using the binoculars as that proximity spotting will be lost when they get a certain distance away.
If you are spotting EVERY enemy before you are killing them, you should have this during the first mission, unless you are playing on easy or normal. If you are spotted, enemies that fire at you on those difficulties are automatically tagged, potentially lowering the total number of enemies you can tag.