There are two ways to place marks. The first uses navigation on the map:
Now boxes will appear on the map. These mark the edges of the quads and usually have the name of the quad inside. If they do not appear, zoom in closer. Now click on the map in the desired area and a mark will appear. The page will reload to do this.
The other way to mark the map is to use the search function:
You can search for a place name or the quad name. The pulldown menu selects which of these your search is. Some quad names are repeated in many states, so adding the state may be required. Press the "go" button and the map will move to the desired location, zoom in, and place a mark.
Once the mark is on the map, click on it. This will pop up a bubble with download links for the available maps for that location.
There may be many maps that appear to be the same map. Some of them will be, but some will have been revised with purple at later dates. To find out about a map, hover the mouse over the date and more information will pop up. Generally, the most interesting bit of information is the photorevision date.
Clicking on the view link will bring up a thumbnail image of the map. This usually works quickly for the first one or two, but can take quite some time after that for me.
Once a map has been selected to download, click the link under the "download" image that displays the file size of the map.
The downloaded maps are in PDF format and are stored inside zip files. You therefore have all the options for printing these that you have with PDFs. If you want it at 8.5x11", you can print it using a shrink to fit option onto a piece of letter paper. If you want a piece of it printed at actual size, then the current view may be printed.
Edit: USGS topos only have a very limited legend printed onto the map. To better understand all the information hidden in the marks of various colors, it is useful to download the full version, which can be found in the publications section of the website by searching for "topographic symbols", or by clicking here if it hasn't moved.