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I understand you are developing customization with j2ee components and not in OAFramework, If you are doing customization in OAFramework then only you might face problems in future.
If you are doing customization on j2ee components, deploy into a CUSTOM_TOP and keep separate and you can use it later also.
Coming to your questions, if you can provide the business scenario , we can provide better suggestion. But for now, there are 2 ways to make changes to standard seeded application:
1. Personalization : A feature of apps where where you can make a lot of changes without changing any code. It is patching, upgrade safe.
2. Customization : Provides a guideline to apply code changes in such a manner that seeded code can be overridden. Again It is patching, upgrade safe if done following the provided guidelines.
For details you can check the OAF Dev guide.