Final Alert 2 does not understand new game modes. You can enable a map for a new game mode by opening the map with wordpad, and putting your new game mode name on the GameMode= list in the map's [Basic] section. Note that if you edit the map in FA2 again, game modes that FA2 does not understand will be removed.
Or, you can do this in the same way that the C-GEN Assault maps work. But your mod would need a .PKT file to set the properties of the maps, and you'd need some sort of mechanism (like a mod launcher) to put the .PKT file into the user's game folder when it is needed and to remove it again when it is not needed.
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