The resources in your test application and your main application are accessible separately in an instrumentation test case. If you want to access resources that are in the res/raw or assets folder of the test project itself, you can use
getInstrumentation().getContext().getResources()
To access resources in the application being tested (the "target" application), use
getInstrumentation().getTargetContext().getResources()
Note, however, that you can never modify files in the assets folder;
getResources().getAssets().open(sourceFile)
returns an InputStream. There's no way to modify the file. That's because assets are stored compressed inside the APK, and are not really writeable at all.
If what you want to do is modify the path to the files the Activity you're testing uses, you should use ActivityUnitTestCase and setActivityContext() with a RenamingDelegatingContext. This allows you to redirect file and database access in a context to a new directory by specifying a directory prefix. You can even use the more complex constructor to wrap the target context for most operations, but use your test application's context for file operations, so the activity will access files stored in the test application rather than the primary application but still use other resources in the primary application.