The master output should be kept below 0dBFS, all other levels mostly do not matter.
Amp clipping (output stage) is very bad for speakers, but that has nothing to do with the input!
Amp clipping increases dramatically the power delivered to the speaker and can damage a speaker very quickly.
The -6dB line is shown as the half amplitude line, i.e 50% not to be confused with -3dB (half power)