Customers have funds held thru preauthorization & then charged thru 3rd party payment proceser.

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We have manual processing set up but we're in testing we're still seeing preauthorization going through and holding funds that sometimes overlaps with charge to customers after actual shipment through our 3rd party payment processor. We can't have the funds held while we're then also charging. Doesn't look like we can shorten the authorization window but even if we could can we not charge at that point? How do others prevent this overlap?