Yes, the big arms on the top are the docking points of the bigger ships. But i don't have any idea for the docking pionts of the smaller ships. So if anyone has a good tip for that, let me know about it.:D
If you don't want to touch animation, just have a place to attach on a vanilla module or two, so you can attach the ones with docking bays to it.
I would also suggest breaking the station up into components and doing them all as separate models, will make hitboxing easier probably and also means your station parts could be used elsewhere in Sirius, attached onto stations like other modules.
I have a question about the smaller ships docking points. They must have a door? coz i have a idea to make the hangars just shielded against the radiation so the ships can go thru the shields but the station is protected from the radiation and vacuum.