You request the upgrades on shuttle usually as if you were using a 500-mile cert -- for example, on UA.com, when you upgrade a shuttle itinerary, you select a 500-mile upgrade.

GA's working shuttle are very well aware of this policy, since, they handle the 1K upgrades on Shuttle on every flight.

I'm sure the computer system over rides it, etc... as a 1K, i've never had a 500 mile cert taken out indavertantly on a Shuttle route.

-Adam