This isn't really a back to back ticket.. a back to back would be if you booked:
ATL to BOS - leave Friday, return Monday $250
BOS to ATL - leave Saturday, return Tuesday
$250
As opposed to:
ATL to BOS - leave Friday, return Saturday
$1000
So for $500, you fly OUT on the first leg of the first ticket and you fly BACK on the first leg of the second ticket. You never fly the last leg of either ticket... and you save $500.
The airlines all say you can't do this. I have, in fact done it, but I ultimately used all segments, and that's a key w/ the airlines.
I frequently have to change my travel plans. In some cases for schedule reasons, I end up w/ a ticket on another airline. On the first, non-refundable tickets, I just keep it, pay to change the return up say a month in advance and end up with two round trips, using two airlines - but not using them sequentially. I got no response from that practice and I've done it a number of times.
In your case, the key issues are that you intend to fly each leg of what you have purchased and that you don't have one ticket that exists to get around the sat night stay requirements while you take another side trip. That's actually 'nested' tickets, and there is a lot of debate as to it's permissibility or ethics (although lots do it for perfectly logical reasons).
I do this all the time for a variety of reasons.. for instance, if an airline is running fare specials from clt to atl and then a different fare special from atl to fll and i'm lucky enough to need to get from clt to fll, as far as I'm concerned I've hit the jackpot! I get a much cheaper fare and more segs to boot! (although segs isn't always what you're after on vacation, the cheaper fares usually compensate for the inconvenience).
Hope I haven't confused you even more.. bottom line is that what you have scheduled, IMHO, is perfectly ethical. I think the reduced point requirement must reflect the difference between non-stop and connections, but that's a guess. If you wanted a 24 hour layover in the second city they would MAKE you do just what you have booked.
Others may have more to offer, but I say go for it and have a good trip!