The following only refers the normal factions AI, I do not care much about the new factions AI in my mod.
At first, I tried to do skirmishes games with my mod that contains new factions and noticed that the AI isn't as always, so I tried to add the new units to the object lists.
And then, after I edit and save it, I noticed that the skirmishes aren't as always also, though a bit better, I tried to import this to a map, and then the world builder says that it has some waypoints, combat area and etc that are duplicated.
Does someone know what is it and how can I successfully edit SkirmishScripts.scb to get the skirmishes games to work as it needs to?

You cannot directly edit a .scb file. Load it into a map. Make changes by going into Edit/Scripts then export the script.

Duplicate waypoints, objects, and areas can be resolved this way. Allow the scb to place these (answer yes to the continue question), then find them and remove the imported waypoints, areas, and objects. Then go to scripts and find the errant script and save it again, but do not check the boxes 'include waypoints', 'include areas', 'include objects', etc., before you export it. Export the script using the same name.

However, It is good to include named objects when exporting scripts. This way, if you want to use the same scripts, you don't have to place the objects and name them. They will be imported for you. You'll then have to move the objects to where you want them. This is a time saver. For example, lets say you have a handful of name civilian infantry on your map and the script uses these named people. If you export the script and choose to include the objects, the next time you import the script, the objects will be placed and named for you. All you have to do is move them to where you want them on this map.