CDP has many processes requiring two input files. In Soundshaper these are normally loaded into two processing rows - A and B. Row A is selected by default but if necessary, click on Row A, then import a file by drag+drop or file menu, etc. into cell A_0. Then similarly click on row B and import the second file into cell B_0. Re-click Row A if this will be the primary source.
Select your process using the menus. A red box appears on the left side for selecting the 2nd source. Simply click on cell B_0. Then click OK in the box. If you are using spectral processes (for formant applications), both files should be converted automatically to spectral .ana files, behind the scenes. Select parameter values and click RENDER. The result should now be in cell A_1 - the next in the A row.
A simple example is CROSS, similar to VOCODE, which replaces the spectral envelope of the A sound with that of the B one. If the A is more static and the B rhythmic, you get a good result.
A word of caution: CDP expects the two files to be of compatible type. Processes won't work if one is 24-bit and the other 16-bit, for example. If not sure, click on the cell and select CTRL+I for file information. All CDP spectral processes are natively mono-only, but Soundshaper can handle stereo files. I tested my CROSS example with a mono sound B modulating a stereo sound A and this worked, but I can't guarantee this for all CDP processes, unfortunately.
In Soundshaper's Patch grid, each row is a chain of processes from left to right, and the last cell in a row is the latest one for that chain, ready for the next process. When using two or more inputs, the 1st (or main) input will always be the last in its row, but the secondary ones can come from any cell, even one earlier in the same row. For example, if the source is in A_0 but the processed output in A_1 is significantly quieter, you might select LEVEL | BALANCE then click A_0 as the second input. This would balance the original and the processed sound.
Further information can be found in "Soundshaper Basic Operation", a pdf available from the "Graphic" page in the CDP online documentation, which you can access from the CDP website.