Based on your description, yes, that’s how you’d model it to capture the benefits of reusing the existing structure.
With regards to your second question, general layout drawings that show the areas that were retained and which areas were demolished or new-built will be sufficient evidence. However the lead author should also provide some workings/material take-offs to demonstrate how you’ve arrived at the assumptions/quantities you’ve modeled in eToolLCD (i.e. your calculations on how you arrived at the % of structural components retained).
I hope that answers your question.