I run my 8 outs to individual channels on my mixer, and eq each independantly, add separate effects, etc. The main advantage is that you have a dedicated mixer summing all sounds together and individual control over each sound.
The Stereo outs sum everything through a simple mixer / amplifier combo, so the sound quality is better with the individual outs. I usually separate like sounds to the same output, like all kicks go to 1, all snares 2, hats, 3, toms or claps and shit to 4, and then depending what other samples I have I will spread them out, trying to group sounds in the same pitch range on each out so the eq settings can stay about the same.
I rarely use over 6 of them at a time, but it is very handy.