As far as I know, .NET doesn't have anything built in to directly support sending FAXes via a FAX server. Absent that, you'd probably want to use the COM interface to the fax server. Basically, you create a FaxServer object and invoke its Connect method to connect to the FAX server. You then invoke the FaxServer's CreateDoc method to create a FAX document object. The FaxDoc object has a (huge) number of properties to specify more about the recipient and document than any sane person would imagine, but the two main ones are the FileName and FaxNumber. Once you've set those (along with any others you want) you invoke its Send method to send that document to that fax number.
I last played with this a few years ago, so I'm probably skipping a few things. Mostly I remember that it seemed strange that the FaxServer created a blank FaxDoc that you filled in and then asked to send itself, and that there was a lot of documentation covering "stuff" that initially seemed like it would be necessary, but turned out to be completely irrelevant, at least for what I was doing (and in retrospect, probably usually would be).