You will be good with a balcony - don't stress about the junior suite. We booked our cruise as soon as it was available and were able to snag a good price. Reading these boards will give you a good idea what to expect.
Since you haven't cruised before - I recommend bringing along some Bonine, found at Walmart. Our trip in the open ocean between Washington and then back in the protected waters north of Vancouver Island was quite rocky. So much so that my fitbit was registering activity even after I was asleep. The rest of the trip was like glass but those few hours surprised me. Bonine doesn't make you drowsy like Dramamine.
Also, if you are looking for excursions, I can't recommend Jayleen's Alaska enough. We had a wonderful day of whale watching on her smaller boat out of Juneau.