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Hydrus is not excellent at paged content. I hope to improve this in future, along with more general cbr/cbz support. For now, try adding 'page:1', 'page:2' and 'chapter:10', 'volume:5' and 'series:blame!' style tags. It takes a little effort to set up, but you can often regex-parse these from your original file import filenames. Then, in the client, set it to sort files by 'creator-title-series-volume-chapter-page'. This will line things up nice, but the workflow, particularly for editing things once in the client, is not as I'd like it.
inbox/archive is a hardcoded special 'tag' that works like your email inbox. New files start 'inbox', with the little envelope icon, and then if you decide you want to keep a file (e.g. it was not some garbage you downloaded by accident), you hit F7 to archive it. The system:inbox/archive system search predicates let you filter by these statuses, letting you set up a 'filter this new stuff' page or 'look at this good stuff' page. It is just a neat way to keep track of new and verified 'good' files. Check out the 'archive/delete' filter as well, as per here:
https://hydrusnetwork.github.io/hydrus/help/getting_started_files.html