the .ncs must be de-compiled first...
Did the 2 mods include their source files (.nss)? This would be want you want in order to edit/combine the scripts.
You can attempt to de-compile the .ncs using the DeNCS Script Decompiler (
http://www.starwarsknights.com/tools.php#sct).. the program should work in either K1 or K2 now, depending on the version of Java (JRE) you have running..
However, you'll still need to 'manually' combine the 2 scripts once you have their source.. it's just getting to that point is the biggest problem.. hehehe
If that doesn't work, post which 2 mods you are using, or the byte code for the .ncs :)