If you only want to change the position of the buttons than that will not be a great deal. I meant to say that it is pretty easy.You will only need to change the position of the block.
Go to the layout file i.e paypal.xml which is located in "app/design/frontend/base/default/layout/paypal.xml".Here you should search for the code snippet
<reference name="checkout.cart.methods">
<block type="paypal/express_shortcut" name="checkout.cart.methods.paypal_express.bottom" before="-" template="paypal/express/shortcut.phtml">
<action method="setIsQuoteAllowed"><value>1</value></action>
</block>
</reference>
Here change the "before" text to "after".Now you can check on frontend and you may see that the paypal button shows after proceed to checkout button.
One suggestion of mine is not to make changes to the core file.First overide the paypal.xml file to your own theme and then make changes to it.It is the best practice.
Hope this will help.