Major Renovation vs. New Construction

We are working on a library project that involves the renovation of an existing facility, and the addition of a new wing. Both are included in the LEED scope of work, and all existing mechanical equipment will be replaced as part of the project. (The addition will double the size of the existing building) I initially labelled the project as "Major Renovation" and indicated the amount of "Addition Floor Area" assuming the excel template would pro-rate the EAp2 credits achieved. However, when I change the addition floor area there appears to be no change in credits awarded. Does this mean the template is calculating points based solely on the "Major Renovation" requirements alone? Our energy modeller wants to provide his own excel sheet that will pro-rate the credits based on square footage of new, and square footage of existing, but this means our LEED document will not accuretely represent total credits achieved. Any thoughts on how best to approach this? (This is based on the CaGBC's version of NC2009 - my apologies if there is any difference w/ USGBC)