Yes, you can manually rate and fulfill orders in FlavorCloud.
Note, you also can re-rate orders that have previously been assigned a shipping rate and fulfilled. If the order has already been fulfilled and you would like to re-rate it, you will first need to cancel the original fulfillment. Please see here for how to cancel the fulfillment of orders. Also note, if you re-rate an order the shipping rates may be different from what you charged your customer at checkout.
Step 1: Select the order to be rated
Click on the order number of the order you would like to manually rate. This will open a new window with the order details.
Step 2: Rate the Order
In the order detail screen click on the "Rate" link at the top right, and then follow the instructions on the screen to rate and fulfill the order.