Manually you can do it by right-clicking on the graph and selecting to see the graph legend...now expand the legend to show the number of graphs you have, then click on each of the curves in the legend and you get a menu where you can set the color and lots of other properties of each curve.
Programmatically you do it by making a property node linked to the graph with the "Active plot" and "Plot color" properties...
Attached is a picture of an example...in the example I also set the names of the plots programmatically. On the front panel you can see the graph legend where you could have done the same changes manually.