Hi Phoenix,
The rows in Soundshaper's patch grid are chains of processes, each going from left to right. So your source should appear in A_0, not A_1, and when you've processed it, the output will be in A_1. (A_2 would be for the output of the next process, if any, not for the second input.) For your second input, place the cursor on cell B_0 and drag your second soundfile onto the screen (or use the file selector). Click again on cell A_0 and select the process that requires a second input. A red "ADD INPUT" box should appear. Click on cell B_0 to select it and click OK in the red box. If your process is spectral, B_0.wav will be automatically converted to B_0.ana behind the scenes.
Set your parameters on the parameter page and click RENDER to return to the main page. The output should be in cell A_1. For a spectral process, this will be colour-coded aqua and should again be auto-converted back to .wav to play it. However, you can also hit F9 to do an explicit ana-wav conversion, if you like. This would be worth doing if you save the process as a patch, for example.
Hope this helps.
Robert F.