I know this question sounds dumb, but I am unable to understand the difference between the main project and project option provided inside each repository.
Are they same? (But the URL differs)
I looked at help.github.com
but it doesn't help.
I basically understand that for larger projects management, project inside repository is helpful.
on what uses cases, they provided the another project outside of repository and linking those repositories to it?
Is that for structuring?
There is a repository on github (sometimes called a "project") where you store your code. You change the code, make a git commit, and push those code changes to the github repository.
GitHub also has a feature called "projects" which provides you a method for managing the work that needs to be done on the code. GitHub also has "issues", an issue tracker. You can use the GitHub Project Board to organize your GitHub issues, giving you a way to see see where things are at in your effort on the code.
You can turn off the "projects" and "issues" features in the repository settings, you don't have to use them. The center of work is the code in the repository, which might be referred to as a project -- the Projects feature lets you manage your issues in GitHub in a more visual format.