The 5 Master EQ settings are provided to give you the best possible sound when listening through different reproduction systems-
the instruments internal speakers (1 and 2), headphones (3) and external speakers (4 and 5). This is a good addition because headphone/lineout single jacks don't always sound as good as dedicated line outs.
In my testing, setting 1 and 2 accentuate the bass so that the internal speakers sound really full, which I already reported on. Now, with my outputs plugged into a pair of powered monitors, settings 1 and 2 are very bass heavy but when I go to 4 and 5 the EQ curve sounds great. I also confirmed the headphones sound better when using setting number 3 compared to the others. Yamaha did us all a favor here!
Kaye's Music Scene