You're welcome for the quick response. But don't feel foolish. This is my issue, not yours.
I should have mentioned that each volume/takubon and chapter/issue listed
is a separate book using this method.
You're thinking of having a one-to-many database structure. Where you would enter one unique book title and then have multiple volumes/chapters associated with that title. So, one title, many volumes.
I'm simplifying here, but calibre stores books on a per title basis (really, it's per internal id# - but those are based on title entered, so... /shrug). It does not allow a one-to-many structure of this type. For books (text) this generally isn't a problem because title verbiage is not re-used word-for-word. However for any type of periodical (manga, comics, mags, newspapers, etc) this presents a problem like you've encountered. The title is re-used exactly, with only an issue # or date differentiating each issue.
My suggestion on how to handle things is simply one method to try and deal with these limitations. By using a uniform naming system with exact placement of elements, everything sorts properly and makes finding a specific book much easier. Comic software might handle things better, but you're using two different programs - increasing the learning difficulty. But they also don't offer the tools calibre has readily available.
Other users may have an alternate method they use for periodicals and similar situations.