SSL and dedicated IP

We started our store under https://www.minigrid.com/index.php which is hosted through Bellhosting.ca and they have just installed a new SSL Certificate on a dedicated IP for us. The SSL certificate is from Comodo and it works only if the index page is under the secure folder which is under the root so we again need another copy of everything in our Zen-cart store (under /secure folder and under /public folder) which was the reason why we purchased our dedicated SSL certificate from Comodo. Does anyone want to help and tell us how to install/reinstall or set up our store?
Thank you,
Nesin.

I would first ask them if that couldn't set up your site properly with symbolic links and such so you don't have to maintain two sets of files ...

How do we do that? What exactly should we ask them? Is there anything that we can do using our control panel?
Thank you!