I am a US citizen and have been in Italy since September. I am coming up on my 90 days since I do not have a visa and have to return back in the US. However I will be enrolling in University classes and will have a student Visa in January. Am I required to wait the 90 days outside of Italy before re-entry or am I allowed back in since I will have a visa the second time around? The first entry was essentially just as a tourist so I had no visa.
Assuming that the visa you're getting is a type D (long-stay) visa issued by Italy:
The visa will allow you to stay in Italy only without complying with the 90/180 rule relative to your earlier stays in the Schengen area. So you should have no problems if you travel directly to Italy when you re-enter.
If you're going to transit through a different Schengen country on your way to Italy, things get more complex. The Italian D visa does not in general exempt you from the 90/180 day rule with respect to the other Schengen countries. In principle the rules say you should be allowed to transit through another Schengen country in order to reach the one that issued your long-stay visa, even if your 90/180 allowance is used up, but you never know how easy it would be to convince a border guard of this. So if at all possible, it may spare you some trouble if you make sure not to use up all of your 90 days before you leave for the US in the first place.