the simplest way to solve this is to change the binding for the price that is passed to the cart.
On the product detail page, find the following code:
$ATC_itemPrice = floatval("".$row_WADAProducts['ProductPrice'] ."");// column binding
and change that to:
$ATC_itemPrice = floatval("".$row_WADAProducts['ProductCost'] ."");// column binding
This way the value pof product cost will be passed to the cart instead of ProductPrice.
You could use eCart to mange things as well, but that will get much more difficult.