We're going to Chicago in March (from MAN via ATL) and the flights were booked for us by a company who use a travel agent. I'd planned on upgrading the flights with some miles as we were booked into Y with an E fare code, but when I called FC I discovered that a booking made through a travel agent can only be altered through the travel agent, which is a real nuisance! As we never use a TA ourselves I was unaware of this. I was told, however, that we might be able to upgrade at the airport depending on availability; we'd just have to pay the difference to an upgradeable fare and then any extra taxes/fees, as per usual. Has anyone done this before with this type of fare class? The flight doesn't look terribly busy on Expert Flyer so I am hoping at the very least we can pay to upgrade to PE even if rewards seats aren't available.
In theory anything is possible at the airport. If there are spare seats there's every chance they'll sell you one but of course it's never guaranteed and flights can fill up last minute, particularly on a route like ATL which gets a lot of late corporate bookings.
VS are right though I'm afraid - they can't touch bookings made through travel agents until T-24 and as a general rule they can't be upgraded with miles.