Credit Card Process when there are multiple shipments against an order

We are using the Authorize.net plug-in 

Our typical business process is:

1. Authorize the entire amount of the sales order - say $1,000
2. Create shipments. There often is more that a single shipment because we ship certain items from one warehouse and others from other warehouses. Say the authorization amount is $1,000
3. We invoice the first shipment and we are triggered to Capture via Credit Card Processing for Sales (SO.50.70.00) - say $800.00.
4. When we invoice the second shipment there is no trigger to capture the second shipment for $200.00. It seems that the remaining authorization does not transfer to the second shipment/invoice.
5. The result is that we are releasing invoices that have credit card terms but have a balance

I’m thinking that the credit card system does not allow for authorizations to be split.

What would be the best business process to ensure that we are capturing the remaining balance on the second invoice?