Welcome to the GitHub Support Forum! I’ll be happy to help you get started.
So, you’ve created your first local repository which corresponds to a folder on your computer. You said that the files that you’ve modified are not the ones in this repository/folder?
If I’m understanding you and that is what’s going on, you’ll need to replace the files in your local repository with the updated files of the same name. Upon doing so, you’ll notice that some changes happen in the left-hand column of GitHub Desktop showing which files have been updated as illustrated in the help documentation for Committing and reviewing changes to your project.
You can then use the checkboxes to decide which files you want to include in your commit which is a collection of changes packaged together. Once you’ve done that, you need to add a commit message at the bottom of the left-hand column and hit the button to Commit your changes.
You might find the full documentation for Contributing and collaborating with GitHub Desktop to be especially useful. Since you’re new to GitHub and Version control, I also recommend checking out the First Day on GitHub Learning Path in GitHub Learning Lab and the Hello World guide to learn about the concepts you’ll be using with GitHub Desktop.
Please let me know if that’s helpful and if I can help out further. Thanks!