"The main issue is that your cart page URLs include your store id, but it is encrypted."
But GA has the ability to overcome that.
http://www.google.com/support/analytics/bin/answer.py?hl=en_US&answer=72285
When you setup the goal...
Goal Type = URL Destination
Match Type = Head Match
Goal URL = /sc/thankyou.cgi (the folder depends on where you installed your SS cart)
Case Sensitive = Unchecked (but I think this doesn't matter with ShopSite)
Goal Funnel Step 1 URL = /sc/order.cgi (same on folder name, depends on your install)
Goal Funnel Step 1 Name = Cart (or whatever you want to name it)
Goal Funnel Step 2 URL = sc/billing.cgi (same dealio on folder name)
Goal Funnel Step 2 Name = Checkout (or "Show Me The Money Jerry")
You may have other pages in your funnel depending on how you've configured ShopSite, but the Head Match choice will let you deal with that.