Erson,
Lighting Controls are factored into the lighting power density as required in Appendix G Table G3.2. For instance, you can claim a 10% reduction in lighting power density if you have an occupancy sensor in the area and your facility is larger than 5,000 sq ft.
If your installed watts is 1.0 W/SF and you have an occupancy sensor, then you would enter 0.90 W/SF in the EAp2 table in question.
If you want to claim more savings than that, you need to use an exceptional calculation methodology and explain and justify your baseline and savings calculations. Even then, you would enter the installed watts (unadjusted) in the table, and claim the savings for controls in the Exceptional Calculation Methodology section. This is often done when a project team has a daylighting study they're basing their savings on.
The final approach is to enter a "Whole building" W/SF and use your calculated watts per square foot from Energy Pro for the entire building.
Hope this helps,
Paul