It is best to think of the input modules as capable of routing 8 of the SSP input jacks. This is because 1 through 4 and 5 through 8 of the input modules inputs correspond to jacks 1 through 4 in a row on the SSP. So while you could select the first jack in each row in the input module, this will give you a summed version of all 4 of those jacks. This is intentional as you might want to sum inputs like this.
So when you want to use jacks 3 and 4 on the first row, and jack 1 on the 2nd row, you would enable input 3 and 4 on the first row in the input module, and then jack 1 on the 2nd row. On the output section of the input module you would use the 4th encoder to select which ones the input module is sending out. From the example above we have inputs 1, 3, and 4 to work with. So we would enable outputs on those numbers. (In my case it was usually 3 - CV, 4 - Gate, and 1 - Y movement.)
It is a very powerful module, and its abundance of scopes really help in setting up patches however you want.
The only way 1 and 2 would be summed is if you route them to the same input of a module. IE: if you route 1 to pitch, and 2 to pitch on the WTO, they will be summed. Otherwise they are not summed as they are completely separate signals.
Yes you could, BUT it will be 4 separate signals with each signal being 4 different signals summed into one.
The WTO, LFO, and Granular (to name a few) need to be tuned when using cv control. (Via MIDI tuning is automatic, but you can still manually tune for specific tunings, etc.) When loading new samples into the WTO, you will get the same pitch that was previously there. Tuning through the 2nd and 3rd should only work if the module is not receiving any pitch data from CV or midi. Is this what you mean?