The way that the PowerStore works rite now is that when you add an item you are just adding it to the database. The items themselves do not have any connection to the cart.
On the pages that have the add to cart code and button a recordset is used to pull the data from the db. You would need to either alter the add to cart page to include your code, or create a table in your db where you can hold the new code you need to use and just reference it with a recordset.
The PowerStore is a PHP based site, so you can edit any part of it to be like how you want. It would be up to you to determine how exactly to integrate your other cart into it though.