I want to create a variable hostname.
I copied the first sites virtual user profile to create site2 and created a new server for it and changed the hostname to be http://www.site2.com
However, when I change the site2 virtual user nodes it also changes the shared containers url's as well. is there a way to have to share the containers?
The very nature of a Shared resource is that you can make one change and it will effect all scripts using it. This is not what your intended desire is fundamentally. You need to have two similar but independent sets of transactions.
One way to achieve what you want is to instead COPY the container with the transactions you want to have available for the other script. Make the changes globally for that script, but this way they will be independent instead of Shared.
Let us know if one of these solutions help.