As explained on the manual, GSX will do an actual refueling or not, depending what has been set in the airplane configuration at the "show fuel and cargo dialog during refueling" option.
If the option is enabled, GSX will refuel, which means it will fill the fuel tanks, using the DEFAULT variables.
So, if the airplane you are using use a custom fuel system (not using the default tanks), even if you set the option, GSX won't affect it so, you don't have any other choice than disable the option and let the airplane refuel itself.
I don't know the airplane you are referring to ( I believe A2A does several models ) and none of them are included in the GSX configuration so, either you configure them by yourself, or use a pre-made configuration made by the airplane developer, who might know better how their fuel system works.
