You should leave the master fader at 0 dBFS (i.e., untouched) and try to achieve a maximum peak between -6 and -3 dBFS by balancing your channels. If you aim for each channel to peak at -12 dBFS, you will usually end up with plenty of headroom on your master bus.
If it's clipping there and your mix is otherwise good, you can lower the overall volume with a gain utility plugin until it stops clipping before exporting or rendering to a WAV file. The only thing that matters is that the master isn't clipping. All this "leave 3 to 6 dB headroom above peak for audio mastering" is nonsense.