File one:
angular.module('myApp.controllers', []);
File two:
angular.module('myApp.controllers').controller('Ctrl1', ['$scope', '$http', function($scope, $http){
}]);
File three:
angular.module('myApp.controllers').controller('Ctrl2', ['$scope', '$http', function($scope, $http){
}]);
Include in that order. I recommend 3 files so the module declaration is on its own.
As for folder structure there are many many many opinions on the subject, but these two are pretty good