In order to use Jar files you’ll need to build some custom java actions to interface with them. You can then import jars in Eclipse and use them in those java actions just as you would in a regular java project.
See the Mendix eclipse documentation for a quick tutorial on how to import the project in eclipse and run it for debugging purposes.
Hope this helps.
Place the jars in the userlib directory and deploy for eclipse. In eclipse write the java-action and the jars can be invoked. It is the easiest way to paste your code and let the autocomplete of eclipse suggests the jar to import.