There should be badging on the vehicle showing either Limited or Custom. The Limited came with the following four factory options on every model: cruise control, dual power seats, cassette, and alloy wheels.
As to why an auto part store would ask, I dunno. Both models have the same engine and transmission. I can only guess the more equipped Limited might have different parts for some areas of the vehicle, but when I looked online I didn't see any difference when browsing starters and alternators.