In your layout update
<checkout_cart_index>
<reference name="checkout.cart">
<action method="setCartTemplate"><value>path/to/your/cart.phtml</value></action>
<action method="setEmptyTemplate"><value>path/to/your/noItems.phtml</value></action>
<action method="chooseTemplate"/>
</reference>
</checkout_cart_index>
chooseTemplate will choose the right template