Alright so I play an Epi Special II and when i play with heavy distortion, i have the tone switch down (treble) which i believe is the bridge pickup? And its sounds great but when i switch and try to play in both pickups it sounds a bit muddy. It really only sounds good i play clean, a little bassy though. Any thought on what the problem might be?
The neck pickup (the one marked 'rhythm') has a lot more bass and mids to it and less treble. When you're playing in small spaces, bass tends to drown out treble and mids always comes through the most no matter where you're playing. So neck pickups often sound muddy when you're using a lot of gain and playing at home or at practice. The bridge pickup has less bass and more treble so that sounds more even. When you use both pickups together in the middle position the neck pickup usually dominates the tone so that will be muddy too.

There's really nothing you can do. It's just the nature of guitar. It's hard to get a neck pickup that can take a lot of distortion and still sound clear, unless you put a really thin-sounding pickup in the neck but then that sounds bad when you play clean. You just have to live with it. Remember that when you get to play in larger places the balance between bass and treble can be a bit more even.
Never heard a guitar that sounded tight through distortion in the middle or neck position. Middle and neck sound best when played clean or sometimes when soloing. Nothing wrong here.
I'm gonna have to agree with the above two posters. You dont have a problem at all. Thats just how the electric guitar is inclined to sound. You aren't going to get a tight non-muddy sound on your middle pickup selection.

Normally I use my bridge for all my riffing and heavy stuff and I use my neck for some clean stuff. Of course this is up to preference. But hearing some mud from your middle and neck pickup positions is normal.
(Gear in profile)

Yes I do like metal, no I'm not a close minded idiot.
You can change the sound of the pickups by raising and lowering them using the screw on either side. Lowering adds more bass to the mix, but reduces output.

Also, Epi pickups leave a lot to be desired. But as others have said, you will not get a great distrotion out of the neck. Although, you can get an EQ pedal to help tailor the sound to your liking, and also, P90s can be very nice for a more full hard rock crunch in the neck. I believe guitarfetish makes humbucker sized P90s. If your trying to get metal distortion out of the neck, well you are really just out of luck.