There are several options depending on what tools and skills you have.
1) using PersonalEffect Print server and the APIs, a programmer/developer can link an eCommerce site to uProduce to push form values into an InDesign or XLIM document on uProduce and get back JPG proof or PDF output. This is the cheapest (in terms of software purchase) and most flexible solution - but it requires development skills which may increase the overall cost of the solution, and mean that you have to continue developing the solution over time.
2) using PersonalEffect StoreFlow (which includes uStore - XMPie's eCommerce solution) might be a little more expensive in terms of software, but uStore offers a store type called "uStore connect" this store type is designed for integration with other ecommerce systems. I know of developers who have integrated StoreFlow with eCommerce solutions such as Magento (and others). In fact, XMPie Professional Services can even sell you a Magento Plugin that sets up the uStore<->Magneto integration. This allows you to have native Magento products in the store, and enables you to add products that come from uStore. Using StoreFlow and integrations from XMPie Professional Services mean that you benefit from ongoing product development and upgrades and support (while on a support contract) without having to continually update a custom-built solution.
I recommend you contact your XMPie Account manager to setup a meeting/demonstration with XMPie presales and/or professional services team to see what is possible and discuss your requirements.