There are help pages that come with the product that share the details of launching .NET programs outside of VTune analyzer and other such details, but the basic thing you want to do is find out where your webapp is spending most of its time. This "hot spot" analysis collects real data about what functions are taking time; those functions should be the place where you should concentrate your attention to optimize the code. Hot spot analysis is done using the event sampler collector, which collects data about any programs that happen to be running at the same time. That means you can start your webapp, start driving it with requests, and then use VTune analyzer to figure out where the work is being done.
There's another aspect to testing that I just alluded to. In order to profit from event sample collection, you've got to make sure that other than VTune analyzer, the only other heavy activity on the system is your webapp. This means driving it with a sufficient load that most of the samples come from the webapp, or from some pathology that indicates a bottleneck somewhere else.