The final decree should incorporate the PSA which means that the terms of the PSA have the same weight as if they were written in the final decree. Virginia Code Section 20-109.1
Courts are quite happy to incorporate a PSA into a final decree unless the court believes the PSA is not in the best interests of any children of the marriage. If the terms of the PSA do happen to be in conflict or the decree does not have language incorporating the PSA, speak to your attorney immediately.
The Final Decree of Divorce is controlling, but if your Agreement was incorporated into the Final Decree and there are discrepancies, then you have an inconsistent document which probably should be addressed, depending on the nature of the inconsistencies.
The Final Decree of Divorce is the controlling document but if the Agreement was incorporated into the Final Decree, it is part of the Final Decree. If your Final Decree and Agreement conflict with each other, you will probably need to address the discrepancies depending on the effect of the discrepancy.