Thanks for your help so far, may as well keep at it! Have got some more info - a topic here on setenv applies, it turns out - but still stumbling along.
Have tried loads of software etc, but now thinking of NetBeans - am told the setup is auto/easier, and it creates packages and directory structures needed based on the code, and that it will help me via reusable classes and methods.
any opinions here? If I try one more thing, I want it to be the last!
I don't think an IDE is the right solution to the original problem.
The issue is that OS X uses different directories for certain purposes than Linux or some other flavors of Unix. I think if the original poster finds the correct corresponding directories, the original problem will be fixed.