Vacuum is usually used for fixturing flat things, like plywood. It sounds like you're expecting it to hold onto the bottom of a fairly tall thing while you machine on the side of it. I really doubt that will work very well; the force of the tool plunging into the side near the top is likely to break it loose, or at least shift it a little. What you need for that is something like a "tombstone" fixture, which needs solid fastening to the workpiece - that or an awesomely powerful vacuum pump.
When using a vacuum pod, it's normal to mask off the area not covered by the workpiece; this conserves vacuum pressure that would otherwise go to waste, and concentrates it where it's needed. The "shared area" would be the surface of the pod that's covered by your part; the rest would be masked off.