I fly basic economy all the time and it's hit or miss for whether I'll be able to choose a seat at check-in. Generally my flights aren't long enough to worry about a middle seat being bad, 1-1.5 hrs.
If all of the standard economy seats are taken ,and only preferred seats are left, do a dummy booking to check, then you won't be able to pick a seat at all. You'll be given a boarding pass with seat assignment at gate. In general I don't mind this, as I'll either get an exit row seat or closer to the front of the plane, which I like.
Other times I've been upgraded on a BE ticket when I checked in <an hour before take off because all of the economy seats were assigned. But I've also been given a seat in the back of an MD88, with no view and loud AF engines. It's a bit of a gamble. But for my short regional flights in the South East it's worth it to not pay extra.
I'd advise against paying to get a specific seat unless you have a long flight or short connection.