SEO Rule #1. Never hire a company that cold-calls you are cold-emails you. People who do SEO real well typically do not need to seek work.
Michael, please allow up to 2 business days for a response on pre-sales questions. I will address that for you today.
CDSEO when installed initially will import any custom meta data and after that will override X-Cart when the page loads for customers. Meta descriptions aren't a ranking factor so wouldn't have any impact on rankings and wouldn't result in a penalty either. You seem to have over 6500 backlinks originating from 5 domains almost all with the same anchor text, which is likely triggering a Penguin penalty. You should start by removing the link to
www.istok.ca in your news as it could be the likely culprit.
Jack, CDSEO is compatible with Rich Snippets Module as of CDSEO 1.9.1 released yesterday. I've contacted you on skype with regard to licenses.