Ajax toolkit confusion over different versions of Visual Studio

Hello,

I am converting a VS 2008 website to VS 2012 and I am confused about the AJAX control toolkit.

What version of the toolkit should I run in 2012?  The version coming over from the 2008 site is:

<addassembly="AjaxControlToolkit, Version=3.5.40412.0, Culture=neutral, PublicKeyToken=28f01b0e84b6d53e"/>

Also has anything change when using the ajaxcontroltoolkit and what is and how does it relate to NuGet.core?

I must have inadvertently brought in two versions of ajax in 2012, because I have two sets of AJAX controls in my tool box.

How can I drop one and keep the correct one? 

Thanks