Generally speaking, when people have engine problems from mods and such, the root cause is either: 1. A sub-par tune. 2. Driver error. Most commonly, it's a combination of both.
There are certain things you shouldn't do, like lugging the engine (foot to the floor, in high gear, at low speed) for example. While that usually isn't going to grenade your engine, lugging on a crap tune most certainly can cause damage. There is a good "First Time Turbo Owners" thread that covers a lot of these kind of things. Once you begin to understand how your driving habits can cause conditions such as overboost, the safer your engine will be. I've seen people blow up brand new, bone stock STi's just by driving like an idiot.
That said, the tune is the major deciding factor in engine health.