The plans haven't been finalised yet, however you should be able to use your Southern season or day ticket on the Underground between London Bridge and Southwark, Waterloo, Embankment and Charing Cross, also between Cannon Street and Embankment.
It's also likely Southern ticket holders will be allowed to use London Overground to Canada Water and then the Jubilee line.
Those using Oyster PAYG in theory should be charged the National Rail fare rather than the more expensive TfL/NR Zone 1 combined fare if changing at London Bridge or Cannon Street.