I'm going through something similar thing with 2CO. There are two distinct ways to approach the problem.
First, you can sell the product through different web sites in which case you need an account for each site.
Alternatively, you can have different web sites for each product if there is one web site that has all of the products listed. It is this web site that is associated with your account.
If someone visits one of the niche sites and wants to purchase the item, then the transaction MUST be handled through the primary web site (where all of the products are listed) because it is the one associated with your account.