Perks are little boosters you can give your hero each time you've meditated to the next level in one of your temples. They are things like giving your hero an increased chance of finding tech points or consumables, getting better at fighting with certain weapons, travel faster over the map etc.
You can find them on the hero tab (gold crown at the top of your screen), under skills (gear icon on the left of the screen).
If you've meditated to the next level, you should see a green button saying "stats up" on the skills tab (if you haven't meditated yet it will be yellow and say "reskill"). Click on the green button and you will be able to assign two skills points to the general hero skills (hover over each of them with your mouse to see what they do), and one perk point to a whole range of different perks like I described above.
They are definitely worth using as they will make you faster, stronger, wealthier...
