I've done EXTENSIVE modifications and am using Smarty for other areas of our website including a VIP lounge and online learning locker, so that the xcart database can be used for other aspects of the site. I also created our index file in smarty so that we can have a login on the main page.
I have:
index file in ./
store in ./store
learning locker in ./locker
assessment tool in ./locker/assessment
and I can't put the assessment in ./locker because eventually we will have too many of them.
What I ended up doing was creating a second smarty.php, changed all the links and setup the templates to reference ../../skin1. I then had the php files in ./locker/assessment reference this second smarty.
The site is LIVE and is located at:
https://www.crgleader.com/