First of all, it looks like you have two three separate storages. Even with separate HDDs (multiple repositories), you could have pointed all three repositories to a single storage, and benefited from greater de-duplication.
Not to worry, but you’re gonna have to pick one of those storages going forward (the largest?), as unless you created the others with add -copy
(copy-compatible), you won’t be able to merge them.
But with this new-found knowledge that you can have multiple repositories (from multiple computers, even) backing up to a single storage, you can see that it doesn’t really matter how you organise your source data. Yes, you can have a single repository backing up all three HDDs (or pool), if that’s what’s easier. Or you can keep the current one repository per drive (or current structure), or create as many base directories for as many repositories as you want.
It will all de-duplicate, with minimal re-upload. (Aside from the fact that you can’t merge those storages, so you will have to re-upload 2 of the drives after picking one of the storages as your main storage going forward.)
You can and should, of course, keep the deprecated storages around until you don’t need the historic snapshots any more.