Yes, this is an old thread, but for the sake of those who surf in via Google like I just did, here's my recommendation.
I put together my pedalboard to accommodate two separate signal paths.
First, I use an ABY box which has a single input and splits into an "A" loop, a "B" loop, or a "Y", and then blend "A" and "B" back together into a single cable to the amp with a resistance mixer.
The "A" signal is continuous, but the "B" is the Wah->OD->Noise Gate loop.
Clicking on the "B" button turns on the Wah->OD->Noise Gate while the "A" loop is still active, preserving my original unaffected signal.
With this setup, I keep my Dunlop Bass Crybaby, OD pedal, and Noise Gate on at all times and just toggle the "Y" with the "B" switch.
This solves the problem that many bass players have—they lose the bottom end when they use the wah. Mine has blistering overdriven wah and the original, unaffected bass signal underneath. It's a dream setup.