As I was making a delightful grilled turkey, ham and cheese for my wife, I kept thinking about this and some other odd thoughts crept in. We have to assume that the Back-up Prime was in the event of a catastrophic failure at Prime. Based on that assumption, it is likely that Project Planners with intimate knowledge of the restoration plan would be there. Then there is that problem with the Counsel of Tomorrow and their families. People that sacrificed so much for the Project, we cannot assume they would be left out to die.
So based on those assumptions, Back-up Prime might be the base where the Counsel was to sleep out the war with the planners with two objectives. Wake up when restoration is well underway to the cheering of a grateful nation or to try and patch together some kind of restoration given the first plan failed for some reason by working with what is left.
This still has a few gaping holes. If this were the case, then Prime can wake up Back-up Prime anytime with the appropriate code. But how does it wake up in the event of a failure? Was it suppose to just automatically wake them up 20 years later assuming a problem was severe enough to not allow Prime to wake them? If so, what happen to that clock? Was it a second disaster or sabotage?
But to Sgt's questions, I see the Back-up Prime as smaller and designed to coordinate pieces rather than be a supply and support base. Prime Base was meant to monitor and record events and then to gather intel and activate bases. The Back-up had no one awake to monitor, so they are relying on either the data sent to them by Prime or whatever they can gather for themselves. If we assume that it is the Counsel and their families, there would likely be a large(ish) MARS contingent for protection or insurgency to try and free up otherwise isolated or harassed teams.
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