Add the ajaxtoolkit registration to the web config. It will then be available in any page or user control. Add it after compilation section:
<system.web>
<compilation debug="true" targetFramework="4.0" />
<pages >
<controls>
<add tagPrefix="ajaxControlToolkit" assembly="AjaxControlToolkit" namespace="AjaxControlToolkit"/>
</controls>
</pages>
</system.web>
Also remember to add a reference to the dll.