Only one beacon URL can be specified, and you should put that in the View Cart code on every page of your site, so no matter which page the buyer orders from, the cart on that page can pass the beacon URL to checkout.
As I recall, you're not selling any digital goods such as downloads, correct? If so, you may want to try the method "If you are selling only tangible goods" explained here:
http://www.e-junkie.com/ej/tips.tracking.conversions.htm
That should auto-redirect buyers to the thank-you page after checkouts on PayPal's site, and of course card-based direct payment checkouts always auto-redirect regardless; however, I think Google Checkout still doesn't provide any way to auto-redirect to any thank-you page after completion of checkout.