Ok, sounds like both are fine when kept separate but integration has not been so great for people. Because our finished CMS site is already Joomla, i'll keep that and might just do a separate store with Magento.
However, I might also look for a small Ecommerce addon for Joomla since we won't be selling much. I'm just not sure i trust the security of Joomla with credit card info and such.
Anyone have experience with a dedicated Joomla Ecommerce solution that can comment on that part?
Thank you again everyone.