Donal
Set it up during the day and leave it running over night and have a minimum of 2 machines, so when its tied up running simulations you can still get on with other stuff.
Depending on number of zones that sounds pretty reasonable to me. I've had energyplus models I got bored with letting them run after 4 days. Ok its quicker now, but the Apache bit of IES is always a bit quicker than most. The issue comes when you start to take account of the Outcast and Radiance calculations for daylight linking control, all of which energyplus does at the same time as running simulations.
You should obviously take the time into account if you are setting up model, etc but I'd be very surprised if you can get away with charging for computational time. CFD people can get away with that as they are tying up processors for long periods often right across a network and it often does take longer.
Just my own opinion of course, but I'd be surprised if anyone on this list gets away with that. If you do, please don't tell me, just well done to you...;-)
Regards
Dr Paul Carey