Using a meteorite is the default behavior, that is, you change locally, and the result is saved on the server.
Now that the scene can be quite large, you will most likely have to update the whole json, but using the key path Scenes.update("sceneid", {"$set":"some.path":"value"});
You might also consider creating a scene editor as a json editor or something more advanced understanding of the three.js syntax. If so, if you know AngularJS, I would recommend using AngularJS on top of Meteor, using any graphical json tree editor (or your own editor), just bind the scene to the scope using $scope.myScene = $scope.$meteorObject(Scenes, sceneid); , add the 3DJS tool and you're done.
Inside the code page, you will have a json tree graphic editor that can edit any json document (this is your scene) and is synchronized with your db server. That is, every small change in the json structure will be applied locally, but also sent to the server and change the MongoDB scene record.