
The good news is that a larger alternator, within reason, will not damage or cause problems with your electrical system but there are some things to do and look out for.
The voltage regulator in the alternator controls the alternator, the voltage regulator can make the alternator put out little amps or alot.
The voltage regulator measures the state or charge of the battery and turns the alternator up or down depending on how fast the power is leaving the battery (current draw). You might have a 250 amp alternator that is only putting out 25 amps because that is all the system needs, then as demand goes up the voltage regulator turns the alternator up. If the voltage regulator fails in a way that allows the alternator's output to go out of control can damage your system.
One of the big factors with high output alternators is to make sure you have large enough battery wire and an upgraded ground as well.
A wire that is to small that runs between the alternbator and battery will for sure damage your alternator.
Large wires, good grounding throughout the whole system and a good battery are most important.