Hi Flynn. Take a look at the sticky topic, "Using Adventure Cycling GPS Data" at the top of this discussion group and the link it gives to the GPS Data User Guide on the web site. You will find many of your answers there. Briefly, though:
You do not have to rename any waypoints unless you want to make them more meaningful as you ride with the GPSR showing the next waypoint name.
The waypoints and GPS routes that you load into the Etrex will be visible. TransAm contains 3406 waypoints, more than the 2000 limit of the Etrex 20. You can deal with this in two ways: reload part way across or winnow the waypoints at home before you load up, using the receiver's auto-routing to navigate between the remaining waypoints. Alasdair wrote about this in http://www.adventurecycling.org/forums/index.php?topic=10425.0
The 65 GPS routes in the TransAm download contain the map section number in their names. (GPS Data User Guide describes the naming convention.) Each includes 25 - 30 waypoints along the cycling route. You can use them as they stand, planning to begin and end each day in the middle of a GPS route. Or you can use them as a basis for creating your own routes.
I agree with your assessment of the Garmin manual. It is also lacking for us experienced gadget geeks. Look around at http://gpsinformation.net/
for better tutorial material. It is a large and interesting site; plan on a few hours there.