Back to the OPs issue - how I deal with anthologies and journals.
I have a 'related/Related" long text column, with HTML, Header on the side attributes, this is where I put the inter-book links.
- Add the anthology/journal as a book, if necessary convert it to EPUB.
- Use the Epub-Split plugin to create the books for the individual stories/articles
- Put a list of calibre:// URLs referencing the individual stories/articles into the Related column of the original anthology/journal - usually view-book links, but sometimes show-book links or both.
- Put a show-book link to the original anthology/journal book into the Related column of each story/article book.
The clipboard extender I use (ClipboardFusion Pro) makes this waaaay easier than it would be if I only had the normal Windows clipboard.
Added: For journal PDFs I sometimes split it into article PDFs rather than convert to EPUB and splitting that.
BR