My EQ is set flat on my guitar and my head.
Supplying the experienced SWR users here with the exact settings on each control knob of your amp would be helpful.
As to your rig's head overpowering its cabs? You could always be grateful for the extra power amp headroom your bass amp now has and turn its volume knob down a bit to compensate.
Here's an interesting piece written by Rick Jones at Acoustic Image on the subject of amp power and speaker loads:
The Purpose of Power
http://www.acousticimg.com/manuals/The purpose of Power 8.pdf