This week's book giveaway is in the OCPJP forum. We're giving away four copies of OCA/OCP Java SE 7 Programmer I & II Study Guide and have Kathy Sierra & Bert Bates on-line! See this thread for details.
If the application is in an executable jar file (it's a jar file that you double-click to run, or that you can start with the command: java -jar TheProgram.jar), then you have to add the external classes to the classpath in the manifest file of the executable jar.
If I create another jar containing updated files only, how can I refer it in the original code?
Short answer: As long as the new jar is on the classpath, it should work.
Long answer: It would depend on how the "patch" works. Does it involve code changes to your original classes? Does it involve new classes? If yes, how is the original jar supposed to use the new classes without any changes to the original code? Anything else?