Charging and collecting additional fees after initial purchase?

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We have a standard store where people add items to their cart, pay for them and then have the order sent to our fulfillment system. All good so far.

We want to offer some new products where in addition to the original purchase price we need to collect other fees based on things that happen during our fulfillment process.

So a customer buys something for $50 but during processing calculate that we need to get an additional $12 from them. Our customers know this can happen and that we can't calculate the amount until it hits our backend, they just need a way to pay.

Can I add something to their cart to represent the $12 and send them a notification to pay it in shopify? After talking to their support it sounds like it can be done but it would require someone manually doing all of these steps.

Anyone have any experience doing this in an automated fashion, and if so, which API should I be looking at?