I was excited about this on my Alaska cruise in 99. Alas, you will be lucky to see darkness! Our first night out of Seward there wasn't any night at all! According to a good friend of mine who grew up in Alaska, the northern lights are more of a winter show. (I suppose it has to be dark to see the lights in the sky) Of course we went in May, so maybe in September you'll have a better chance.
I may be wrong about this, and if so, I would appreciate clarification from someone who knows for sure, but from what I have read, unless you go into Interior Alaska (Fairbanks or north of the Arctic Circle) I don't think you can see the Aurora Borealis. In any event, unless it's dark outside I don't think it's possible to see the lights anyway.
Good that you are going in September. That's the best time to POSSIBLY see them, when the days and nights are more equal in length. Of course it depends on conditions. I remember reading a report from a passenger who saw them last September from the deck of their ship. I didn't see them when I was there in mid September unfortunately. It was cloudy and rainy that week.
Not likely to be seen. You need dark nights and no clouds. Be out on deck 2-4 am for any sightings, perhaps you could see if the pursers desk will call you if they are sighted? Depending on when in Sept you are going it is not an ideal time. Keep checking independently for price reductions which have been heavy in the past few years. I take my second yearly Alaska trip then for the rock bottom rates, I have not paid more than $500, but it is indeed a trade off compared to May- Aug sailing.
I just got word from reliable sources that those of us in California may be able to see the aurora tonight as far south as San Diego. Check out this web page for a "heads-up" on your own potential for seeing it. The solar flares are real heavy right now. If you have a clear sky, try right after dark tonight!