Im new to Magento and in doubt how to process an order when there are products sold out. My Magento is set up to automatically process the payments from within the order. But what should I do when there are products that are sold out? I will invoice the products that i can, but then there will still be a part of the payment left and my order status is still "processing". How do you normally handle this situation?
If you want to invoice and collect payment for all products, then invoice all of the line items, and raise a separate shipment for just the items that you're shipping out now. When the other products are back in stock, raise a second shipment for the remaining products.
"Processing" means that the order has been invoiced, but not fully shipped. If you use two separate shipments as above, the order will live in the "processing" state until the second shipment has been created, at which point it'll switch to "Complete". This is the normal Magento order flow. The Aligent team has drawn a complicated looking diagram showing the complete order state flow which might help understand what's happening.