I'll try to help since I was an audio person before getting into cameras. First is to understand the differences between a stereo mic and a shotgun mono mic. It really is like comparing a 35mm lens and a 200mm lens in many respects.
Stereo mics are generally good for sound sources that are fairly close and also when you don't want to isolate a particular sound source, but you just want to capture everything there in it's natural balance.
On the other hand, a shotgun allows you to "zoom in" on a particular sound source and to at least some degree "crop out" what you don't want to hear. Of course just like different length lenses, different shotguns will "isolate" more than others, the general rule being the longer it is, the more it will isolate.
So (as ususal) it comes down to what you want out of it. As for brands, the Rode and Senheiser stuff is very good as those companies also make high end studio mics costing thousands.
Based on what you say you want, you can probably rule out shotguns since they are all mono. I'd probably lean towards the newest Rode stereo mic even though it's on the upper end of your price range. It will be easy to use and sound very good. (check out the "product demo" link at BH for the sound of this mic)
As for camera settings, you're in very good shape with the 5D2 since it can either be set to auto where it will adjust itself to the proper level (none of this type of adjustment is all that great but will suffice as long as the sound levels are at least somewhat constant), or you can set to manual and adjust the "volume level" while looking at the meters that will show up in the LCD.
The only other thing I'd offer, which isn't completely related, is avoid trying to shoot handheld. It's almost impossible to get usable footage without some sort of stabilization with these cameras.