The main Gecko window has buttons down the left hand side and across the top. The left column buttons spawn external readers like this one. The rest control the simulator.
Scenarios has a list of preset examples to run. The first ran automatically when you started Gecko.
To stop a simulation, click the next button, Pause. It's a good idea to pause before setting up something else to run. Continue goes on from wherever the simulator is stopped, even if it ran to the "end" of what it was told to do. Step 1 and Step 10 are provided for convenience in watching a bit of simulation carefully.
Restart goes back to the beginning of the current simulation, without reloading the original protocol from the Scenarios menu.
RunControl items take effect immediately, during the current run. It sets how often the statistics plots and main circle display are updated, when to stop the current run, and turns on assorted statistics plots. Note that you can get rid of any statistics plot by clicking on its window close icon at the top. However, once it's closed, you can't get it back except by selecting a scenario again.
Parameters are generally referred to once per run. After changing any parameter, you should select Restart. Selecting any Scenario will go back to the protocol, not your hand-edited parameter values. Parameters include the size of the landscape and species characteristics such as how many are born and what size. You can't add species, but you can set their initNumber to 0 to get rid of them.
Statistics plots can be zoomed in or out. Rubberbanding a box upwards zooms in on that area (at least until the plotter needs to grow the plot area.) A downward box fits the current whole plot into the box indicated, zooming out. Clicking without rubberbanding a box restores the plot to normal full display. Plot windows can be grown, including to full screen. Clicking on the close icon gets rid of the plot, and it won't come back unless you select a new Scenario. On some statistics, the x-axis is time and the y-axis whatever quantity is on the title of the plot. Others are entitled "Y vs. X", with "Y" and "X" giving quantities for their respective axes.
The main circle display is just a display. Depending on the browser, that window may look horrible if you resize it. You may zoom in the display by mouse rubberbanding a box, as with the plots. Clicking on the window (drawing a very small box) restores the original full-fit display.
If Gecko gets really ill, use [Shift]Reload on Netscape or [Ctrl]Refresh on Internet Explorer, to really restart it. Unfortunately, this also reloads the simulator over the net.