I believe there is no definite methodology, it is all experimental and dependent on the applications you are running and as Valdis told on the changes you would like to make. Basically, when a paper offers a new algorithm or design then they should have tested it on their own testbed. They may report their experimental methodology in the paper or even have the experiment scripts on the Github. However, other than the applications, and your changes, the testbed itself is also important. Their system may work with a CPU frequency different than yours. So you might not see the performance gain as they reported and achieved in the paper.
For instance, concerning some network enhancement in TCP stack, some people may improve the end to end latency just 10s of microseconds and you suppose to capture those minor microseconds in your experiments. It is really hard but not impossible, it basically takes time and effort + *extensive evaluations*.
I know that nowadays system software papers are pretty practical, and they try to build a working systems. I'm particularly talking about SOSP and OSDI papers.