You'll have to play through each of the 4 different paths for this achievement, I've linked in some videos below which will breakdown which puzzles can be found on each path so you can keep track of what you've done and what you need to do!
The System Override mini-games are very easy once you've got the hang of it, your first playthrough will be the hardest because you'll be unlocking equipment as you play but if you decide to playthrough again and go for this achievement you'll keep all the equipment you've unlocked (you unlock it by just progressing through the story).
There's not a great deal I can advise you on this game type, however I strongly recommend that you pay attention to the tutorials before each "new" System Override because they'll explain the new "software" that will be available, how to use it and what it does, there's no real consequence if you can't beat a particular game first time so don't get too worked up if you're struggling, keep calm and keep trying making sure you're using the equipment you have to it's full potential.
On subsequent playthroughs you'll find these games infinitely easier because you'll be able to spam out pieces of your equipment that you didn't have access to on the previous playthrough!
* Credit to RoosterTeeth for the videos