Without seeing a picture it is hard to say but general you can seal off the pipe using an expansion plug
https://www.amazon.com/Rubber-Winte...qid=1476626389&sr=8-2&keywords=expansion+plug
You can get them at Home Depot or any hardware store. As far as the lines having water in them they can freeze so it's best to blow them out then cap them off. Can you drop the water level down below the pipe inlet in the skimmer? If your skimmer has a weir on it take it off if you can, there might be a spring with a pin on it that slides to move the hinge a little. The box should be fine but if there is a name on it then contact the company that made it. Why are you keeping the pond going all winter?
https://www.amazon.com/Rubber-Winte...qid=1476626389&sr=8-2&keywords=expansion+plug
You can get them at Home Depot or any hardware store. As far as the lines having water in them they can freeze so it's best to blow them out then cap them off. Can you drop the water level down below the pipe inlet in the skimmer? If your skimmer has a weir on it take it off if you can, there might be a spring with a pin on it that slides to move the hinge a little. The box should be fine but if there is a name on it then contact the company that made it. Why are you keeping the pond going all winter?