As it says "put two more damage counters", it adds to the 3 already being placed by Toxicroak. As such, 5 damage counters are added between turns.
Relevant ruling:
Virbank City Gym
Q. If a Pokemon has a poison condition that places more than one damage counter per turn, like from Crobat's "Ultra-Toxic Fang" attack, does Virbank City Gym work or not?
A. Yes, it works. You place 4 damage counters for Crobat's "Ultra-Toxic Fang", then you place 2 more for Virbank City Gym making a total of 6 counters placed. (Feb 28, 2013 TPCi Rules Team)