File Movement Question

So I got an Apple TV and an external harddrive with around 550 gigs of media. I thought you could just plug it into the Apple TV from the box, but when I realized you couldn’t we set up the files (fat32 format) and connected them from the HD to a Mac to the ATV.

So now I discovered the aTV Flash and am going to purchase it. My friend is putting the files into the journaled HFS format (I think that’s right?) and I’m going to mod the aTV today.

Most of my media was not purchased off of iTunes or anything like that, and I had to separate movies and TV shows on iTunes on the Mac before it showed up that way in the Apple TV. My question is, when I set it up so that it goes right to the external hard drive, how will I separate the files into their appropriate places?

I’m really not good with any tech stuff, so the simplest explanations would be the best. Thanks!