I have a ton of TV shows and Movies and in the old Media Center (Vista) i could just browse by folder, now they show up all clumped together in Movies? is there anyway to change to where I just see the folder like before?

Just use the Video Library and you get the folder based view.

the videos are not showing up there?

Have you added the file locations to the video library?

The movie library and the video library are separate areas and can monitor different folders.

Right click when in the video library, or press the i button the remote and click on manage library, add the desired folders, click yes, use these locations and click finish.

You may need to back out of the video library and then go back in to see the new folders show up.