selecting the 64gb SSD or outdoor viewable screen only takes off the Windows Tablet PC OS option that includes a case & pen, giving you XP Pro or Vista Business to choose from.
That does not mean it is not an active digitizer screen, which you would have to purchase a wacom pen separately.
It is possble OQO decided not to provide a pen abled tablet screen, but their site & news releases does not say one way or another. I'll ask and report back if no one else does.
As far as storing the pen, the belt clip case has a place or you carry it like any other pen. No built in pen silo, wish there was.