1) Use a payment processor that supports partial capture. 2) Only capture when the shipping is complete. 3) Do a full capture, and refund promptly if you/sell

1) Use a payment processor that supports partial capture. 2) Only capture when the shipping is complete. 3) Do a full capture, and refund promptly if you/seller can't ship the rest. This is technically not allowed but some merchants/platforms get away with it. The "prompt refund" part is very important, you don't want to end up with chargebacks.