Shopify have finally answered our clients prayers and added manual orders to Shopify!
You can create orders and send invoices directly from your Shopify admin. This lets you handle purchases in a few different ways:
create new orders and enter credit card payments in Shopify for sales you've made by phone, in person, or elsewhere
send invoices to customers to pay with a secure checkout link
use custom items to represent additional costs or products that aren't displayed in your inventory
sell products at discount or wholesale rates
take pre-orders
Check out the full documentation over on the Shopify manual.