Yes, you should be all right, on the grounds that you want to stay for more than a year, and you're intending to (or maybe already will at the same time) submit an application for Residence.
And once you get your application for the partner-sponsored temporary work visa in, they should let you have an interim visa to cover you in case they haven't got it processed before your WHV runs out. It's probably a good idea to point out in a covering letter when applying that your expiry date is very close.