It's multiplicative, not additive. So if you have -789% to Drain, your needed Drain is multiplied by .211. If you have the level 3 Drain achievement (-600% Drain PE needed), your needed Drain is multiplied by 0.4. So in this specific example the cost would be (1000)(.4)(.211) = 84.4% PE needed, which is less than the 100% that it begins with after T3 is broken.
I've never tried to get these to that level of bonus or peeked hard at that part of the source code, so I can't say for sure, but I'm fairly sure that you have to first break T3 even if you reduce Punisher Effectiveness needed below the 100% that they start with.