I just purchased the Zeikos fisheye lense for my 50mm Nikkor lens and when I attach it, it doesn' take fisheye photos - just regular with some distortion around the edges... am I using this incorrectly? I'm fairly new so not sure.

There are a series of small brass "buttons" on the outside bottom of the lens where contact is established. If a new lens, there may be some dirt or grease on them preventing contack. Wipe lens and camera buttons carefully with a lent free cloth and retry. Then it is time to go back to the seller.

You don't. The Zeikos attaches to the front of lens with a 52mm filter thread, which then attaches to the D90. If you have the 18-55mm lens, for example, this will fit onto the front of that lens, effectively converting it to a 36-110mm lens. If you have the 18-105mm lens, this won't fit onto it.
This device is really intended for use with cameras that don't have interchangeable lenses. With your D90, you're much better off using another lens instead of putting this onto the front of another lens.

That depends on the lens in question.

50mm f/1.8 AF-D:
http://www.nikonusa.com/pdf/manuals/lenses/AF/AF50mm.pdf

50mm f/1.4 AF-D:
http://www.nikonusa.com/pdf/manuals/lenses/AF/AF50f1.4D.pdf

50mm f/1.4 AF-G:
http://www.nikonusa.com/pdf/manuals/lenses/AF/AFS50G.pdf

Sorry, but the D40x lacks an autofocus motor, depending on the lens to have one. Nikon calls such lenses AF-S. This particular lens does not have such a motor, relying on the camera to have one. The only 50mm lens currently available with an autofocus motor is this one:
http://www.nikonusa.com/Nikon-Products/Product/Camera-Lenses/2180/AF-S-NIKKOR-50mm-f%252F1.4G.html

Earlier this week the Nikon web site listed a new 50mm F1.8 lens with an autofocus motor, but then it was removed. Hopefully they will officially announce this lens soon.

This is done in the menu system. Where you change to mode to Close focus. Read the Manual/ If you do not have one www.nikonusa.com

The D3100 can't autofocus with this lens. The D3100 does not have a focus motor, depending on the lens to have one. The AF-Nikkor 50mm doesn't have a focus motor, depending on the camera to have one.

To autofocus, you need lenses designated AF-S.

As it isn't really a very special lens, I wouldn't pay for a repair, which is likely to be more than the lens is really worth (you will get back a repaired second-hand lens, which might go bad again). Better to put the money towards a nice mid-range zoom.

There is no such thing. You can see a full list of current Nikon lenses at
http://www.nikonusa.com/Find-Your-Nikon/Camera-Lenses/index.page

You can see a list of current and old Nikon autofocus lenses at
http://www.bythom.com/nikkordb.htm

You'll see that no 50mm Nikon lens has ever had VR.

Having received no response in over a month, I assume this is no longer a problem.

Make sure you set the aperture ring on the lens to its smallest setting (largest f/number) and lock it. Without doing so, the lens will not communicate properly with the camera and thus you will not get the autofocusing.