On version 7 of the ParaEq, we've added the option to make the boost circuit independent of the equalization circuit. But it's disabled by default. To enable independent operation, do the following: 

1) hold down both the boost and bypass stompswitches when plugging in the power. The LEDs should flash momentarily.

2) Hit the boost stompswitch. The boost LED should come on. This indicates independent operation.

3) Hit the boost and bypass stompswitches at the same time to exit advanced configuration.

You can also change whether the ParaEq is true bypass or buffered bypass. See the manual: http://assets.empresseffects.com/manuals/paraeq.pdf

To see what version of ParaEq you have, see here.