From AC's news release:

Air Canada and Canadian will not initially be merged. Both carriers will be operated separately, providing choice and distinct brands. Seat sales will continue and the frequent flyer points of both airlines will continue to be honoured according to their respective programs.

There will be reciprocal code sharing on the flights of both Air Canada and Canadian Airlines, permitting passengers to continue to support their choice of frequent flyer program.

Canadian Airline's network will eventually be part of Star Alliance.