The data for the map gets read from a simple XML file, it can be anywhere on the file system where your webserver can read it, just make sure the config file points to the right location. A sample data file has been provided in the tar ball.
A sample single point map is shown below:
<points>
<point>
<lat>-33.8667</lat>
<long>151.2000</long>
<type>visit</type>
<title>Sydney</title>
<country>Australia</country>
<href>http://flickr.com/photos/ripienaar/tags/sydney/</href>
<linkimg>/visited/images/19397064_a15dadd4cc_s.jpg</linkimg>
<comment>Visited in 2000 and 2001</comment>
<linemember>1</linemember>
</point>
<points>
This is pretty self explanatory at this point, I won't go into full detail of each bit of data, the only fancy thing here is linkimg and href these two are reliant on each other, it will show a image that you can click on to go to the URL. If you do not want a clickable image, you can use linktext instead of linkimg, this will give you a textual hyperlink.
The type links back to types created in the configuration file, there is a special type called none that will not make any clickable point, this is to enable line drawing between points without putting markers.
You can put many markers on the map, I've created a map with 2000 points and while it works on big computers it definitely runs into problems on smaller computers, you'll need to do some tests if you want to make really huge maps.
A reasonably good source for coordinates can be found at http://www.fallingrain.com/world/. You could also use the same method you used to get the extend URL's to find coordinates using Google Maps, just pull the coordinates out of the URLs you obtain.