Create > Translation and deep cloning

We’ve used “Create > Translation” on one of our sites in the past to create a copy of it for another locale. We had to edit our Translation and FolderContent relationships in order to enable deep cloning. Now we want to create another copy or our site for third locale, but since the size of the site is much smaller this time we would like to selectively copy sections of the site rather than the whole. We’ve been running into issue with using “Create > Translation” not at the Site level in that the copied items end up in the originating folders.

Are we going about this wrong, should we not be using “Create > Translation” or do we have to undo the deep cloning configurations?