After testing the mod for a while I found out how the ctOS-Boxes work:

1. Hacking minigame
You can simply disable the minigame by unchecking the "Should it use hack interface?" option on the tool.

2. Wiring
Left-Click to place ctOS-Box -> Left-Click on Box to start connection -> Left-Click an entity (like Lamps, SCars, Turrets) to connect box to entity. Each time you hack the box, all entitys attached to it will be hacked too. For instance, if you connect an box to two combine turrets, hacking the box will disable/enable both turrets.