The multiple shipping address process initially creates a single checkout containing the addresses, shipping rates, and tax. Once the order is paid for, it is split into an order for each address selected during checkout.
The initial order that comes through is tagged with "ms_order" and should not be used for reporting. The follow up orders that are created have the shipping details, shipping cost, and tax cost located in their correct locations for reporting.
There are a few things that you can do, which you can test to see what will work best in your case:
1. When viewing reports, filter out all cancelled orders by going to Admin --> Analytics --> Total sales --> View report.
Click the manage filters button on the left hand side, and select 'Cancelled' from the first dropdown, and 'is not' from the second. This will give you accurate reports.
2. Giftship has an option under the 'Shipping to Multiple Addresses' section, where you can choose the financial status of the re-created orders as either pending, paid, or voided.
3. Additionally, you can prevent the order from splitting into multiple shipments by enabling the option shown below, although this is not recommended.