By the way, I have another question on that topic.
I'm using Timer1 to generate an interrupt every Xµs that triggers the pulse for the comparator. That means that the comparator interrupt will be triggered just before the other interrupt finishes. Somewhere I heard, that interrupts aren't allowed within interrupts. Is that true? If the Arduino "remembers" that there was another(different) interrupt during the timer interrupt and executes it afterwards, that would be fine because the comparator interrupt only increments a value and timing isn't important, as long as it doesn't forget the comparator interrupt.