In a zone? Tough. You have to manually track them. This is a true pain when you badge Goldside. They have 8 (or 9+) location badges, then plaques, then graffiti, and then river spots. I take out a scratch pad when I start those zones. Worse yet, the graffiti and the river (and the train) are multi zone puzzles. KEEP TRACK on paper!!!
In a zone like Atlas? I just pick a direction and count them off in my head, plaques and badges. Atlas has a lot of plaques. Most zones have 2-3 max. If you finish and do not get the zone accolade and 5 merits you just open recent badges and compare to the zone map. go pick up the one you missed. But make double sure you got all plaques. That gets ugly if you miss one and cant tell until way later.