Once you have a matching cross section rubber seal and before inserting window push fully home all around aperture and cut a few millimetres longer with join at the top. Then lubricate seal with diluted fairy liquid and use a tool such as
this to insert window. I would avoid generally using glue as seal needs to move whilst inserting. You need to end up with seal ends touching each other and slightly under compression to form seal - a blob of silicon glue may help here.
