I think there are numerous ways to normalize the spectrum analyzer. First, remember that neither the spectrum analyzer nor the signal generator have perfectly flat response. For filters, you have to provide a signal using a specific set of cables, and annotate the measured amplitudes at the various frequencies. If your spectrum analyzer has a normalize capability, which is more common on network analyzers, you could use that.
If the spectrum analyzer has dual trace capability, you can make one THRU measurement, and a second measurement with the filter inserted.
With directional couplers, probably not so simple. You need a good procedure, and good theoretic knowledge of the measurements. I think that may be more complex than normalizing a spectrum analyzer.