If you're not operating with an external display, it's not really clamshell mode; it's simply operating with the lid closed. To keep your MBP awake with the lid closed, use InsomniaX or InsomniaT (rebuild for SL) (fix for 2011 MPBs)
I'd be extremely careful about moving a MBP that's not in sleep mode, especially if you have a HDD rather than a SSD. Also, transporting a running MBP in a case isn't wise, as vents can be blocked. It's better to sleep and resume when you get where you're going.