I understood the manual is not yet updated, but the latest version of GSX has a lot more features. And I do not know how to set them up. One of this features are the engines ?
The manual hasn't been updated because, as the release notes said about these new features of the editor, they are not used right now so, there's no need for you to spend any time configuring them, since it will not make any difference to GSX right now.
The engine positions will be used to position the traffic cones, which now only go to the wingtips so, if you really want to configure the airplane anyway, so you'll be "ready" when we'll release an update that will display the full set of traffic cones, just ignore the image in the diagram and use the normal standards of 1 and 2 being the left/right engines on a 2 engine plane, and 1, 2, 3, 4 being the left/center-left/center-right/right engine on a 4 engine plane.
The image will be updated in the update to display different airplane silhouettes depending on the number of engines, so the final version will be less confusing.