You can usually find good deals for Banff if you look around and check the hotel websites. Jasper has less hotels though so it's harder to find good deals. September is the end of high season so prices are still high, but it won't be as busy. If you can, delay your trip to when high season ends to get better prices. Lots of hotels will have dates for their high seasons. You could also stay in Canmore which is 30 minutes from Banff but is still nice and cheaper.
If you want to splurge, eat at the Grizzly House in Banff. Awesome food and experience, but bring a change of clothes as you will leave very smelly. You can hike the mountain in Banff too and take the Gondola down for something to do if you like hiking. I would also recommend renting a canoe in town and doing the lakes. I don't have much to say about Jasper as it has been many years since I've been there.