autocalibration

I have 2 questions about using autocalibration for combined catchments:

In MikeHydro the term "combined catchments" refers to catchments where one or more catchments discharge into another catchment. 

I have a catchment A that discharges to a river flowing through catchment B.  Therefore, A+B is a combined catchment.
I have a stream gauge record for catchment A (gauge a), and another gauge record for catchment B (gauge b) which, obviously, receives flow from A+B.

QUESTION 1:
I can use autocalibration for catchment A based on gauge a.  But how do I use autocalibration for catchment B based on gauge b?

QUESTION 2:
The autocalibration appears to work for streamflows NOT routed through the river channel network, instead using the catchment runoff. How do I autocalibrate using the routed stream flows?

Thank you so much for any assistance you can provide to either one of these questions.

Mariza