You have to set the display preferences for the external monitor while you are running with the lid closed, i.e. in the mode you intend to use it. Then it will remember the setting. I do this every work day with my PB and it works great.
As for heat problems - I haven't had a problem, but just in case, once the external display switches on and I'm running, I open the PB lid about 2 inches.
To close down at night, I close the lid, unplug the display, then the USB keyboard/mouse, wait a few seconds and it enters sleep mode.