It actually depends on where you install the CubeCart program. If you install it in the same folder as your Joomla, it will overwrite what you have created thus far and break the site and Joomla application.
You can, however, install it into a subdirectory, such as /store for example. Then you can simply make a link to the CubeCart page within your Joomla. This will allow you to use the Joomla for your normal pages and then use the CubeCart for your storefront.
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