What Chris said and:
addOns[]=
{
"ATC_Nogova",
"ATC_BIS",
"atc_runways"
};
addOnsAuto[]=
{
"ATC_Nogova",
"ATC_BIS"
};
Both ATC_Nogova and ATC_BIS have an entry in the requiredaddons section of thier config, that points to ATC_Runways. ATC_Runways has no requiredaddons.
It just so happens that ATC_Nogova and ATC_BIS are also placed in the mission, thats why they appear in both. Otherwise, like Chris said, they would be autodeteced (read from requiredaddons) and just added to AutoAddons.
Hope this helps some.