Markers are used for events, e.g. scripting invasions. Markers range from the numbers 1 to 8 and are shown with a slight pink background when they are used. They also have the colours blue, green, red and yellow which enabled you to have 32 unique markers on your map. This should be more than enough for any events you will need.
The above image is how markers look when they've been added to the map. The colour is the colour of the marker, the letter is the first letter of the marker colour (possible values are B, R, U, G) and the number is the marker number (between 1 and 8). To add a marker, select the colour and number you want, then press control and left click where it should be placed. After you have placed a marker, it can be deleted by selecting it in the marker menu and clicking the "delete marker" option down the bottom.
Once you click a marker that is already placed you will be directed to that marker so you can view where it is on the map. This eases the debugging a lot when scripting your map.