Hi Cabrell,
You cannot build an app in Mendix and then continue with the Java or .NET code outside of Mendix.
That's because your Mendix model needs the generic Mendix Runtime to run.
If you want a scaffolding tool and afterwards continue with the traditional code, you have to go for a traditional programming language.
If you are looking how to interact with Eclipse, you can find documentation about Eclipse here: https://docs.mendix.com/howto/monitoring-troubleshooting/debug-java-actions/
Yes you can deploy and edit your application in Eclipse.