Connect new project folder to github desktop

I created a new repository on my github desktop and choose my project folder. However, instead of using that project folder, it created a new folder within the project folder and has that new folder linked to github instead of my project folder with all my files. Basically, it created a new folder INSIDE my github desktop folder, and I don’t understand why. Can someone please help me connect my project folder to github desktop? Even if that means I have to restart, can you please help me with the step by step? I have tried every single online direction, and clearly I am missing something. THANK YOU!!