That's my understanding of the program, yes. Give the old one back, start fresh.
And yes, you're likely losing out on a bit of money financially. But first off, you're getting an unlocked phone on an interest free loan. You're free to keep the phone at the one year mark and continue to make payments. You could sell the phone for whatever you can get for it at the one year mark and start over with a new phone, if that's what you want to do. Or you can trade it in, and start over with a new phone. In other words, you have options. And since the loan is interest free, it doesn't cost anything to keep your options open.
You can also get a lower cost plan with your service provider (the "BYOD" plan) compared to getting a subsidized phone from them. This should work out to about $20/month less, and you would even have the option of downgrading that further, since the subsidized phones have a minimum plan level ($70 in the case of Telus).
I think, in the end, it comes out as a wash.
Buying 64GB 6s outright (including AC+, since that's included in the Apple Upgrade) = 1055 + 169 = $1224
Getting a subsidized 6s = 530 up front + $20/month (discount for BYOD) + 169 = 1179
Getting a 6s on the Upgrade Plan = 50 * 24 = 1200
In all cases, you can chose to sell the phone outright at any point, and pay off your balance. Really, the only difference is how much money do you want to come up with up front (from the full price to $50), and do you want to be "locked" to your cell provider (even though you can unlock and port if you want to). And the Upgrade plan gives you a "guaranteed" resale at the end of the year. No dicking around with Kijiji and no show or low-ball buyers. I finally got rid of my Samsung S5. Had one guy try to low-ball me when we met, after agreeing to a price prior to that. Another guy who slept through our meeting, and when I called him, his partner said he was sleeping and they weren't going to go through with it. Plus I ended up selling it for less than I wanted, but by that point, it wasn't worth any more headaches.
Oh, and one thing to consider... To maximize your resale price on your phone, you need to sell it BEFORE everyone else does. That may mean selling it and being without a cool phone for a few weeks. If you sell it after launch day, you'll take a significant hit. The Apple Upgrade should alleviate that issue.
Just my $0.02 (CDN)...
C