What I refer to is using the UnrealFrontend to cook all our maps, by default it only cooks the default map, you can either change your ini settings to alwasy cook certain maps or use UnrealFrontend to select which maps to cook.
Just open UnrealFrontend and go to the ‘Game Launcher’ tab (the others could be also ok, this one just has the full path) and then the Advanced section. From there you specify how to build, cook, package and launch your game. In the cooking section you then select the maps you would like to cook apart from the default map.
This is an example of how to package an HTML5 build (similar on every platform): Html5 build issue - Platform & Builds - Unreal Engine Forums