User stories organzation

I liked your product. Its simple and to the point. I like only appropriate and necessary features and let users innovate further on their own. But I find the application lacking in the efficient way organize the user stories. I like to organize my stories into various modules based on the project. The tag label system is not at all efficient and does not promote efficient organization. What if I have more than 100 stories spread across different application sections, for different users. Things tart to get very a bit chaotic. If we can organize user stories, we can carry forward that organization to backlog and current panes. That helps break down the project and track it with this breakdown.