Yeah it's not the most obvious thing. Here are the basics of how to do it.
First you create your test under Options >> Test Protocol >> New. This brings up the "New Protocol File" dialog. To make my test, and I chose a type of "Speed - Time" in the Type of Protocol secition. In the "method" box I chose "Conconi". In the units box, I chose MPH. If you were doing the standard type (every 200 meters or so on the track) you would choose a type of "Speed-Distance".
Then, once I had created and named this test, I went in and specified all the steps. In my case each step was a 0.1 mph increase and was held for 30 seconds. I named this protocol and saved it.
Finally, I went and actually did the workout and downloaded it to the Polar Software. Then, with the graph of the workout open, I went to Tests >> Protocol Test >>name of my test. This does all the analysis.
One thing -- be sure to download the very latest version of the Polar Software. You can get it on their website. They definitely fixed a few bugs in it.