One of the new application guides with the V4.0 release is
aimed at using EnergyPlus for compliance. It's very new, so the
information is not complete but you might take a look at it. (it's
available for separate download from the EnergyPlus web site -
www.energyplus.gov if you don't want to download and install
the whole system.
You could also look at producing files from the Example File Generator
(under interfaces on the website) though they target more looking at 90.1
compliance than LEED.