My personal experience with BE fares is that the seat gets assigned automatically at T-24, regardless of when you check in. You can see your seat assignment appear by going to your reservation online. As far as I can tell, they assign all BE pax to middle seats at that time, or at least as many as possible. I have never not gotten an E- middle seat on a BE fare, though I haven't bought too many of them for this reason. Now I only buy them for short hops where the BE discount is significant and I don't care that I'll be in a middle seat in the back.