Well I've rebuilt my board so that I can not only engage whole chains of effects at once but also mix chains together.
To do this I used two LS-2 pedals. The first is in the front end, set to A+B mix with the Rottweiler and 6-band EQ on A and the overdrive and phaser on B, while the second is in the effects loop, again set to A+B mix with flanger, chorus, and delay and B left empty to serve as a dry mix with A.
The lines on the front end will be used differently for bass and guitar. They work great!!
For bass:
Distortion + EQ on A, dry on B
For guitar:
EQ on A, overdrive and phaser on B
Here's a couple of images (I've always wanted to make one of those spaghetti and meatballs charts, hope you can read it)

