For most parts of VM2 (category view and detail view) you can create your own templates in the views/*/tmpl/ folder.
Under VM config->config -> Templates
I Can select these other templates but I cannot for the life of me find the one for the shopping cart. I have a need to customize the cart templates and I don't want to directly modify the stock templates to support updates.
Any thoughts where I can change this or if there is another way to override?
/components/com_virtuemart/views/cart/tmpl
copy the files to templates/your_template/html/com_virtuemart/cart and make the changes on these files. After an update you must adapt this overrides.
http://dev.virtuemart.net/projects/virtuemart/wiki/Hints_for_the_use_of_the_template_system
Worked perfectly. Now they live after a VM upgrade!