To run MATR, you need the following:
To start MATR, type java -jar matr.jar on the command line.
When MATR starts up, you'll get a small control panel. Press Create to create a new island. When the island's ready, the other buttons will be enabled. If you want to start over, press Create again; Matr will close any window and give you a new island.
This window contains a road map of your island. Press + to zoom in 2X, or - to zoom out 2X. The practical limits to zooming are legibility. If you zoom in too much, however (so only one grid square is visible) route markers won't appear. Use "zoom to fit" to resize the map to fill the window as best as it can (the map will always keep a 1:1 aspect ratio, so part of your window will usually be left blank).
If you click on the map, one of several things can happen. You control this on the window's "Mouse Click" selector.
You'll see the map is pretty smart about route markers, placing them only where needed, omitting them only if the section marked is zoomed out too far. It doesn't do street names yet (that's more difficult than route numbers).
This is the highway log: an inventory of your numbered highways, with a mileposted list of town line crossings and intersections with other highways. Most real-life state DOT's have a document like this. If you've made changes to the highway system, press "Refresh" to see them on the log.
This gives you a 3-D perspective view of any intersection. It's very rudimentary at this point, showing only grass, sky, pavement and signs.
To move to a new place, set the map to "Move Viewer" mode and click on the map. If the intersection doesn't seem to agree with the map -- are you assuming you're facing north?
The most powerful and complicated of all the tools, the Paver lets you pave new roads, tear up existing ones, or decommission highways. It's still fairly easy to hose yourself with this tool; don't try creating roads that cross themselves, go in loops, and so on.
With the Paver, make sure you pave the road first (select a road type), and then also apply a route number or street name.