All gateways have a window in which you're able to capture the funds. That's commonly known as the authorisation period, or authorisation window. It will differ from gateway to gateway (and can differ merchant to merchant) but the average will be 7 days. Some allow up to 30.
It's important that you capture the funds within the window of time otherwise you won't be able to later. If you have orders that are no longer in the authorisation period you can NOT capture those funds. You'd likely want to cancel that order and kindly ask the customer to purchase again. Consider making a draft order in that case and incentivise with a small discount.
You can set up manual or auto captures in the Admin:
The money never actually left the customer's pocket since the transaction was only authorized. Also note that Paypal only guarantees authorization for 72 hours. Past that point, payment could still fail even though the authorization is still valid.
I have added a pre-order App on my store and the products that I am pre-selling will only be available in about 1 1/2 months. This being said, what about if I duplicate an order instead of a draft order? Will the duplicated order stay in the customer account and will the authorize/capture process begin on the day that the duplicated order is created. I am trying to avoid having to ask customers to do extra steps and keep my sales.
As of today, the orders get automatically authorized but it`s quite clear that I will not be able to capture the payment in 1 1/2 month.
@brimccarthy -- Your best bet might be to enable "Automatically capture payment for orders." under Settings > Payments. If you're not fulfilling the order, then you can just refund the money.
If you want to give the customer the choice to pay later, you can add a manual payment method named "Pay Later". When you're ready to collect payment, open the order and send an invoice from the Payment section. Include a message to pay by PayPal/credit card (there will be a checkout link in the invoice) or another payment method before you can ship the order.