People tend to check in during these times:
Make sure you queue up, don't push in front of other people and DO NOT light your fag in the bus queue. It is not necessary.
There's a handy escalator from Bermondsy street level up to bus station from foot of The Shard
It's on the upper level of the street. Take the stairs from inside the station complex.
People like to queue at these bus stops and you may get a cross word if you don't too!