When to check in: a datapoint
Just checked my wife and I in for a flight that has about 30 unassigned seats. Numerous pairs of open seats, but all in the "preferred" or MCE part of the plane. I thought the system might automatically put us together in a pair, but instead it put us in comically far apart middle seats toward the back of the plane.
Based on this, I'd say a good BE check-in rule is:
If there are both good and bad seats available, WAIT to check in until the last possible moment. The system automatically gives away the bad seats and single seats first, so unless all of the "good" seats and seats together get snapped up by people paying for an assignment/late-selecting main cabin elites, last minute check ins will probably get a better seat.