There are several ways to use this tool. In decreasing ease of use, these are: graphically, from this page, in a web browser that understands Java; from the command line, if you have the Java runtime on your system; or by editing the code if you are a Java programmer.
For General skill points, "Spread Evenly" is the default as in the rules, give the points to all units as evenly as possible each round, "Make 9s" means to add all points to the most powerful unit until that shoots at 9, then any left to the the next most powerful, etc. Select a general special ability, if any. The ones marked with (parentheses) don't have any effect on the combat, they are just there for completeness. Enter the number of tests you want to run in the Rounds: box, and click the "Run Combat" button.
Whether or not ships are carrying troops does not affect the combat, but if you are worried about that, write the Loss Order carefully. So, for instance, if you want to keep 1 loaded merchant ship alive as long as possible, and lose 1 empty merchant and 1 frigate first, write "1M1F1M" in the Loss Order box, and it will be up to you to remember that the last M left is the loaded one.
Enter the number of tests you want to run in the Rounds: box, and click the "Run Combat" button.
If you don't see the pie chart, then you entered an illegal value somewhere. Open the Java console and see if you see any message - or just look over the boxes and see where you typed in an illegal value. This could more user friendly, I admit.
Usage: java CombatSimulator A:force D:force [-r rounds] [-al lossorder] [-dl lossorder] [-debug] [-ag generalpolicy] [-dg ge neralpolicy] [-as specialgeneral] [-ds specialgeneral] Force format -- D:2I3C1A8G4W means 2 infantry, 3 cavalry, 1 artillery, and an 8 factor general in a 4 factor walled city. Loss order format -- 1C2I*C means lose 1 cavalry first, then lose 2 infantry, t hen lose all the remaining cavalry. General policy -- 'spread' or 'focus'. Special general ability -- number 1 through 10.The "-d" option shows a runtime trace, showing each combat as it is being rolled. If you want to know how it works, run it that way.
Among other things you will see this currently does not do coast invasions or straits. (Those will be complex, not as much for the computer to simulate but for the GUI - what if some units are coming by land, others by ship and yet others by strait?) If someone adds them, please write, and I will put the changes here, and give full credit.