When using a single process it's not possible to set different filament values to each extruder. Filament diameter, print speeds, material costs etc. are often very different between material types.
If I could set diameter and speeds for each extruder that would be a good start.
Might belong in the feature request area but it's more of a bug for me than a needed feature.
For now the workaround is to change the extrusion multiplier based on filament diameter but you have to print at the lowest speed between the two materials.