I got this before starting Chapter 3 and mainly just wandering around the city looking for loot. You will know when you reach a Secret Area because there is a musical jingle that you can hear.
Generally to reach a Secret Area you will need tools like the wrench and wire cutters as well as rope darts to reach high places. You should use your focus often and search for hidden paths to get up high and into rooms to loot. This should come naturally if you are fairly good about looking for loot. Look for hidden switches in rooms to open a trap door leading to more loot, usually a well hidden collectible.