How is a waypoint marked? Is there a ground station present at that waypoint? And how are these waypoints named?
Ground based radio navigation (VOR, VORTAC, LORAN, NDB) by necessity have ground stations to handle generation, amplification and broadcasting the signals used for navigation. Here is an example of what a VOR station looks like:
"Table Rock VOR" by ZabMilenko - Own work. Licensed under CC BY 3.0 via Wikimedia Commons - http://commons.wikimedia.org/wiki/File:Table_Rock_VOR.jpg#/media/File:Table_Rock_VOR.jpg
Waypoints that represent these stations will have ground facilities underneath them, but they are the minority of waypoints. Most waypoints are defined as a distance along a radial from one of these stations, so there will be no ground station below them. Other waypoints are lat/lon fixes provided by GPS, so there are no stations below them.
Keep in mind, no matter if there is a ground station or not below a waypoint, their presence is not important to how navigation is performed. Waypoint passage will be noted by needles, to/from indicators, DME mileage changing, or by a points along a magenta line on a map display.
VOR stations are often named by their location e.g. the VORTAC in San Antonio, TX is named "San Antonio (SAT)". Others are named for regional things, e.g. "Ranger (FUZ)", "Cowboy (CVE)" and "Maverick (TTT)" all located in Dallas, TX named after their major sports teams (baseball, football and basketball respectively)