Cian here from Shopify. Great question and thanks for reaching out about this!
I understand that you are looking to take pre-orders for goods that will not be available for a further 6 months. One limitation here is the authorization period allowed for online payments. This is the time permitted between the customer placing the order and you capturing the payment. With Shopify Payments, this period is 7 days. With other payment gateways it may be a little longer or a little shorter. However, the authorization period is unlikely to stretch to 6 months.
One workaround solution that you could explore using would be to create a specific product for deposits while making it clear to the customer that they are only paying for the deposit, with the ultimate full price listed prominently in the product title or description. You could then process the deposit as an ordinary online payment.
You can check out the following link that might be helpful when creating a pre-order product page template: https://help.shopify.com/themes/customization/products/allow-pre-orders
When it comes time for the customer to pay the outstanding balance, you can issue an invoice and create a secure checkout link for the customer:
While the deposit and the balance would be processed as separate orders, they would both go through the Shopify checkout and you would be able to keep a track of things though the Shopify admin.
Hope that helps!