Which way do I connect the cables to output 1 & 2 for a biofeedback scan? Red to red & blue to blue or other way round?

There's no such thing as a Spooky2 Boost - there is a Spooky2 Boost Cable, a Spooky2 Boost 2.0, and a Spooky2 Boost 3.0. Of these, only the Spooky2 Boost Cable requires the user to pay attention to color matching. I assume you're not using any kind of Boost, so this doesn't apply to you.

Depending on whether you plan on using hand electrodes, TENS pads, or flexible electrodes, you connect these directly to the generator using either a Spooky2 TENS Cable or a Spooky2 Extended Cable. Both of these are single BNC cables that divide into two wires, one red and one black (not blue). The TENS cable has straight pins on the red and black wires, and the Extended cable has alligator clips.

Since both of these are single cables on their connection ends, you connect either one to Out 1 of the generator in the absence of a Boost, then connect your electrodes to the pins (TENS pads, carbonized rubber electrodes, sandals, flexible electrodes) or alligator clips (steel hand electrodes).

For Contact Mode, including biofeedback scanning, the red and black colors of the wires are irrelevant.

For more details, please check the link:
http://www.spooky2.com/forums/viewtopic.php?f=83&t=7293