The show gave enough clues about Gus for us to know exactly what he did in Chile.
Hector (Tio) referred to Gus as "the grand generalissimo" aka "the general". So some sort of military back ground.
In Season 4, Ep 8 the DEA is interrogating Gus about Gale's death. This part is very important for 2 reasons:
1. It establishes that Gus left Chile in 1986.
2. Gus mentions Augusto Pinochet, who was the dictator of Chile in 1986. '86 is the year Reagan and the U.S. government asked Pinochet to step down.
You might wonder
"what's the connection?"
Augusto Pinochet was a monster. During his reign thousands of people were killed and tortured.
But more to the point he had super labs built that would create color variant versions of common drugs. For example they created a black colored cocaine that was harder for DEA agents to track.
Pinochet 'sold cocaine to Europe and US' | World news | The Guardian
Does that sound familiar? Gus worked for Pinochet until around '86, got the super lab idea from him, hired a chemist (Max) that the cartel killed, and since then he's been trying to get a Pinochet style super lab up and running. Then he meets Gale/Walt and makes it happen, with the blue meth.