I noticed that no matter how far I'm able to squeeze my back together to get that platform for the bar it still seems to rest slightly upon the very top of my spine (the bone that pops out slightly under your neck).  Even if it isn't directly on it but simply touching it, I am noticing a slight sourness and pain in that area.  It goes away usually by the end of the day, but sometimes lingers onto the next!  I am worried about harming myself here, so I was wondering if anyone could comment on if what I'm talking about is normal or how to prevent it.

Thanks much,
Michael

if it realy hurts then wrap a towel around the bar and the pain should go away

Just do a high bar squat.  You don't wanna mess up your spine.

could always experiment with front squats if you are physically un able to put the bar on your back...

actually try a low bar position if it's hitting the spine right under you neck.  The bar should not touch any part of your spine.  It should rest on the back muscles.  check your form.  Don't add a towel.  That won't do any good if you have poor bar position.
 

Yeah, you're prob right mobley.  If anything I bet he's holding the bar too high.

The bar should be below your c2 (the back bone that sticks out at the top) not above it. Like above posted in the picture.