I asked CS about a similar situation. I was going from ORD to BIS and bought two tickets ORD-MSP (B class) and MSP-BIS (B class) on a second ticket. When the miles posted with only 1 on-line booking bonus I called CS. They told me that the computer figures out that I am actually doing a ORD-BIS and only gives credit for one of the tickets (B class). I was told that if I wanted to make changes there would be 2 change fees. I hope this answers your question.