Hi Kol,
You can use both channels in mono mode. This is the mode I prefer.
First, connect the effects loop send on your amp to Channel A input on the back of th SF-2, and Channel B output to your the loop return. Then flick the mode switch on the back, between the input and output jacks to Mono mode (down).
In this setup the SF-2 is a three channel mixer:
channel 1 is the signal routed through Channel A filter. Adjust the volume of this channel by using the knob marked Filter Gain for Channel A.
channel 2 is the signal routed through Channel B filter. Adjust the volume of this channel by using the knob marked Filter Gain for Channel B.
channel 3 is the original unfiltered signal. Adjust the volume of of this channel by using the knob marked Direct Gain for Channel B.
Overall volume control is adjusted by using the knob marked Direct Gain for Channel A.
There are many advantages in using the SF-2 this way. Firstly you can blend different sounds and get new sounds that you could otherwise not have. Also, you can dial in two distinctly different sounds on each filter channel, and say a third on on your bass, and then easily switch from one sound to the other by turning the volumes of the channels up or down.
You'll soon get the hang of it.
The manual is worth getting. It describes all above in detail, plus it has block diagrams and some useful sample settings for the filters.
By the way, you can also use the SF-2 to feed a stereo (2 channel) amp from a mono source. Just connect the source to either the front instrument input (the gain of which is internally adjustable) or Channel A input on the back, then connect channel A and channel B outputs to the respective inputs of your stereo amp. Flick the mode switch up to stereo mode. Then you can control the sound of each channel via the SF-2 filters (you can be Jaco on the left and Stanley on the right [just kidding, but you could try]).
Enjoy
Peter