In the first tutorial we used the 'Run' command to caputure data while an executable ran. However for server scenarios you simply want to explicitly state when to start and stop data collection. It is also likely that you will need to ask someone else (e.g. operations staff) to collect the data for you and send the data for 'offline' analysis. This video shows you the support PerfView has for these server style scenarios.
It is best to watch the video using one of the high quality links on the right so the text is readable.
You may also be interested in the whole PerfView Tutorial Series.