G'day philabos,
...certainly, you aren't alone in having a few difficulties with your initial 'use' of TransDEM - there are some very 'heavy' concepts to get your head around in order to understand what the program is doing. However, having said that the "good Doctor" has (to his credit) developed a program that can be used by just about anyone without any really intimate knowledge of things geographical, outside of the basics of Latitude and Longitude (which most people should have)...
...have you followed TO THE LETTER, the process espoused in the excellent tutorial provided by TransDEM user; steamboateng, in this thread?...
http://forum.transdem.de/viewtopic.php?f=6&t=57&sid=06fd95683b4263de2cdc92d1b9dd5807...specifically, in your case, you need to click on the link to the "creating DEM maps for a route", which will take you to a step by step guide on how to do exactly what you want to do. Bear in mind, that the USGS Seamless Server, as such, no longer exists and has been taken over by Microsoft (and is now known as the Microsoft Research Maps - or MSR Maps) but that notwithstanding, the new URLs required are covered in the tutorial but the process is otherwise unchanged...
Jerker {:)}