EEM run using"whole site / building" question

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I am usingthe EEM wizard & would like to understand using the "whole site /
building" option. I need a different AC system type for the baseline
comparison & must use this option to change AC system type. If I wish to
compare changes in individual components, other than AC, is it best to
choose them as individual EEM runs & use whole site / building to change AC
& then daisy chain them all together? Or can I use whole site / building for
all the individual elements being changed?
thanks
MIke

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