Hello Sandy,
If you have the level set too high in Hauptwerk you will get clipping (extreme distortion due to the signal exceeding the -1 to +1 signal value range that the ASIO or CoreAudio drivers allow), regardless of whether you've subsequently turned the output down again in the driver's control panel.
I.e. the distortion would already have happened before the signal had reached the driver control panel's level adjustment.
For best possible fidelity you should aim to set the output level in Hauptwerk as high as possible without clipping occurring, then turn it down again if necessary in the driver's control panel. However, with ASIO and CoreAudio drivers it will usually make a negligible difference to quality if you have the level set a bit conservatively (i.e. lower) in Hauptwerk. The level for each sample set is set to -10 dB by default for this reason on the 'Organ settings | General options' screen, so you can just adjust it there to balance the levels for your sample sets according to how you use them, but avoid turning the level up too high there (to avoid clipping). Turning it up above 0 dB is likely to cause clipping for many sample sets.