As an apparel manufacturing facility, with sewing, packing, and warehousing operations, do we need to track and report energy separately? How do we track consumption/reduction for multiple facility processes energy, waste, water etc?

The FEM 4.0 is designed to encourage tracking and reporting of consumption metrics, baselines, and targets by facility types (further broken down between industrial and domestic consumption on both water and energy sections), and not by facility processes, therefore there is no need to separate by facility process.
Optimally the facility should install meters for each "source" type and "facility" type to read this data. In the absence of meters, reasonably defined calculation estimates may be acceptable.