We are pretty unfamiliar with Paypal but are currently investigating using it for our online store.
You should give the PayPal integration and support team a call. You can also checkout the online documentation.
How does this model work for a store which sells items that are in-stock and allows the sale of backordered items?
You will need to choose what payment action type(Authorization, Order) is appropriate for your company based on your over all stock situation. if your goods always ship within 29 days use the payment action type of authorization else use order.
Right now we are only pre-authorizing our orders through the checkout...
Yep same ole thing. Your website will create a PayPal order which is basically a pre-auth for the full amount.
Your fulfillment system should authorize and capture for the dollar amount being shipped at that time. Rinse and repeat until completed.
You will have to tell PayPal to allow child authorizations on your sandbox and live accounts.
You could always simplify the process by only showing the PayPal button if all the items in the customers cart are in stock, not restricted, not drop ship. Your payment action type would be sale and you could auth and capture from your website. However this would depend on how well your site and fulfillment system are integrated.
Cheers,
-D
PayPal Developer website & documentation
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https://cms.paypal.com/us/cgi-bin/?cmd=_render-content&content_ID=developer/home
PayPal payment action types
HTML Code:
https://cms.paypal.com/us/cgi-bin/?cmd=_render-content&content_ID=developer/e_howto_api_ECSettlements