We typically extend standard object, e.g. Company, or configure new, custom objects, which can be configured completely according to your business needs.
This new container is effectively dated, so value sets from previous compensation cycles are stored in it and can be reported on. New values for the current period are either entered manually or imported.
Pulling the values on Compensation forms takes effective dating into account: thus, only those values are pulled, which are valid for a given compensation cycle.