The GEMUS value assignments for extras (such as WHDLoad) are somewhat hidden in GameBase. Right click the game you want to modify and select "Extras...". In the dialog that opens, double click the "WHDLoad" entry. There will be a section "GEMUS Fields" and the "Edit..." button will let you change the value assignments for WHDLoad for that game.
If you want GameBase to never set a specific value and instead always use the one set in WHDLoad.uae (which might be a bad idea, because they might just've been set for a reason in most cases
), you have to edit the GEMUS script. Select the script you use from the GEMUS menu and find the part starting with "
If VersionComment CONTAINS(WHD)". Then simply remove the
Set_CFG_* line that applies to the config value you don't want set.
Hope this helps.