CS Shop sync issue with Quickbooks POS using eCC from Webgility

Hello, I provide Web Strategy to a company in the United States which recently setup a new CS Shop e-commerce site. They also have a retail store where they use Quickbooks POS. i Their web developer tried using the product, eCC from Webgility to sync CS Shop with Quickbooks POS. The problem is, when new products are added to Quickbooks POS and synchronized with CS Shop, **each product variation creates a new product.** So, if I create a "shirt" product in Quickbooks POS that has 3 different colors, it will create 3 separate products in CS Shop. Does anyone have any experience with this? I believe the core of the problem is that CS Shop was not setup to "track product options." I don't think the solution lies in hacking eCC, if that's even possible. I think "track product options" needs to be set recursively for all 1,500+ product in CS Shop. Help!!! :-) Thanks, Eric