So far the on line check in is handled by the same system (if you click on online checkin on the Air France site you get taken to an Air France branded page on klm.com).

I don't believe the booking systems are merged but hopefully when it happens we'll be able to search air france fares on klm.com and vice versa.

Last year I was told by an AF agent at LCY that the integration would happen by the end of this year, but who knows how accurate it is.