Yep, that's exactly right. The USGBC will not accept any sort of custom calculations for WEp1 so they really want to ensure that everyone uses the calculators they provide in the credit form to show that the prerequisite is met before attempting WEc2.
My building was completed after 1993 which in WEp1 I selected option 2, then when I go to WEc2, I cannot adjust the numbers that are set at zero, does this mean I would have to adjust WEp1 to use option 4 to then use WEc2?