Regardless of the method that you decided to use, at the end of the replays, you will have two distinct sets of tables containing the workload analysis data, sitting in different schemas in the same database or in completely different databases.
WorkloadViewer will let you visualize performance over time, as we have seen for a single workload analysis, but this time it will be able to show you data from both workloads, so that you can compare them.
This sort of production load testing is both important and difficult; WorkloadTools makes it easier.