Correct, you should generally only copy the files you want to override over to that directory. The reason is that, when you override a file, if a new update of JomSocial changes those template files, the 'old' overrides will still be in effect. So, you want to only use the overrides on very specific files because otherwise, when you update JomSocial, the new updated files won't be used and instead the old ones will.
Hope that makes sense, and glad we got this going for you!
Thanks,
Alex