Normally when we think about value added, we think of marginal revenue product of labor: how much more revenue does adding another worker add to the firm?
If you assume that the market is competitive, then the MRPL should be exactly equal to what you said: wage, benefits, etc. Otherwise another worker would be willing to work for an epsilon less.
In other words, the "value added" by your definition (their "productivity" minus payments) should be zero. From my experience, researchers measure worker's productivity by wages.
If you want to find where this does not hold, then I guess you'll need more detailed data. Perhaps comparing workers with same job description but different compensation.