There's no specific way to EQ a bass VI... Just as you might EQ two regular 4 string basses differently because of how they sound, every bass VI might call for a different EQ. Lately I've been keeping my bass amp EQ flat, and just using my VT Bass pedal for adjustments, because the pedal is so sensitive to the differences between basses that it requires tweaking when I switch from one to another.
I know that when I use the neck + bridge pickup combination on my Barracuda, I need to boost the lows a bit because the thinness of the bridge pickup kills some of the lows. I think I could minimize this issue if I could get the pickup a little closer to the strings, but right now the height is maxed out. I also think if it had a parallel/series switch, I could get more lows out of it by switching to series....