Yes, we have the option of "Add Order" under the orders section of our admin. You can manually create orders and fulfill them from the back-end. The process to be followed is somewhat like the following:
Click "Add Order >> Select items that are a part of the order >> Select from existing or add new customer >> Enter details of payment and complete the order.
There after, the process remains the same. You can then ship the order, print the shipping label, generate invoice etc.