Andreas,
If you are using LV 6, you should use a vi called "Extract Single Tone". It uses interpolation to find the precise frequency and amplitude of a tone, and increases your accuracy significantly. If you just read the peak value, your values will be lower than they should be.
I wouldn't increase your FFT resolution too much. More points means more time for calculation, and you are more likely to miss information that is very close to your desired frequency. For example, if you have 1 Hz resolution on your FFT and you expect a tone at 500 Hz, but it is at 502 Hz, you will miss it if you only read the value at 500 Hz.
Bruce
Bruce Ammons
Ammons Engineering