The S parameter extraction is HyperLynx BoardSim and LineSim is quite easy to use. You can probably extract the S parameters over whatever frequency you need directly in BoardSim. The ports will automatically be placed at component pins. If you need the ports at a different location then you can export the traces and reference nets to LineSim for editing the net. Here is an article with more details about S-parameter extraction in HyperLynx SI.
If you have further questions, feel free to tell us what you have tried and where in the process you have questions.