Hi,
In the hd11 file, in the additional outputs tab, you can tick the option "Lateral inflows" before running your simulation. You'll get a new item in the additional result file, called "Lateral Inflows Boundaries": this contains the discharge from all boundary conditions, which includes evaporation, at all calculation points. When this lateral inflow is negative, it means that the discharge is leaving the domain, and when positive it's added like a source.
Regarding the second question for discharge within the river branches: a negative discharge indeed means that water is flowing back, i.e. the sign describes the direction of the flow.
Best regards,
Mathieu