I use TotalCommander or Double Commander (Open Source). They manipulate archives almost like folders. Built-in archive mechanisms are easy to use.
With cursor positioned on a archive file, double click or enter and I got "into it". I see and access files and subfolders quite normally.
If I need to modify a file - I extract it from the archive, process it, and restore it - overwrite the existing one.
If I need to remove a file, I simply delete it from the archive
If I need to add a file, I simply copy it to the archive.
For all these actions the programs ask me if I want to update the archive, just confirm and that's it.