| I depends. There's no hard and fast rule, but with that many EQ sections things can get out of control pretty easily. A little bass boost on each of them adds up to a big bass boost that can make things start sounding pretty bad!
If I were you and you were me, you'd be telling me to set the amp the way you like it, and use your onboard pre to adjust as necessary during a performance. Perhaps this is where you find out that your outboard preamp is redundant?
Another thing to consider is that all of the different controls are probably at different frequencies, so your onboard bass boost might be at 80 Hz and your amp bass boost is at 100 Hz, etc. You might like how one shapes your tone more than the other.
In general, though, I would recommend keeping most of them as flast as possible, and adjust each band (low, mid, high, whatever you have available) at one piece of equipment only. | 
