1. Get the user info (email, shipping etc.)
2. Create a wallet (via coinbase API)
3. Get notified when when the payment is completed (using chain.com API)
4. Show order completion or redirect to thank you page.
5. Automatically deposit all BTC to the main paper wallet (optional)
It can be a simple php script (or other depending on the ecommerce script you are using) for $100-300.
feel free to contact me if you need any info or have questions.
It would be a simple way to do it but coinbase and bitpay offers protection, support and are easy to use for a cheap price.