There seem to be a bit of communication gap here.
The title of this forum thread is “PayPal form in new window” and the goal is:
“After hitting the checkout button, I’d like to open the paypal form in a new window if possible”
Now if you click on the “Checkout button” from the shopping cart you will see it opens the a new window for the paypal payment. So from my point of view it’s doing what I thought you wanted it do.
But now you just posted:
“The shopping cart still appears at the bottom”
The shopping cart is going to sit where you want it/place it on a page. So my question to you is what are you after?