I may not be correctly understanding you because it appears you are asking for something which is standard functionality. If so please excuse my presumption.
If two scorecards are not differentiated by a dimension (e.g. org structure) then they will have different KPIs or in some cases share some KPIs.
The structure of metric sets does not have to reflect the structure of scorecards. It all depends on who is responsible for providing the data.
Actuals may be keyed in by one user and targets by another. In this case there would be two (or more) metric sets.
A KPI relating to staff satisfaction may be dimensioned by organisation and appear on every org unit's score card, but be centrally entered by the HR department on behalf of all org units.
In your case if the two score cards have different KPIs you might decide to create a metric set for each. Alternatively you might enter them through a common metric set.