Well, the Quickstart Mode scenarios use the Simple AGC (
http://nassp.sourceforge.net/wiki/Simple_AGC). The Simple AGC doesn't understand most of the stuff used in the checklists, but for my part I don't care (at least not for now) as the Quickstart Mode is intended for users who don't want to use the AGC and the other real Apollo systems that much but do it "the Orbiter way" (i.e. fly the CSM like the delta glider, do burns with TransX or IMFD autoburn etc.).
Cheers
Tschachim