I have done this many times with ESP-r and there should be no reason why you cannot model
a ventilated crawl space in EnergyPlus. The approach I used is to explicitly represent the
crawl-space as one or more thermal zones. If you crawled around in such a space what would you
notice if you looked really closely and then imagined what thermophysical processes
are happening in a craw space at different times of the day/year. Then create a model that
takes these observations into account.

The base of the zone is the ground (use the ground model or at least make up a
construction that is a couple of metres thick). The boundary of the ground is probably
something like a monthly temperature at ~2m depth. The side walls and top of the
crawl space are normal constructions. The craw-space top is connected to the
room(s) above. Is there anything in the crawl space that generates heat - if so
include that in a schedule.

EnergyPlus allows you to setup an airflow network so you would have to do a
survey of the openings and cracks around the crawl space and represent this
in the model. This way you will get at least some of the impact of wind outside
forcing air through the crawlspace.

Regards, Jon Hand