Whenever you add a manual order to your ShipStation account, you can not only have multiple manual stores, but you can also choose to have these orders automatically forwarded in sequence. You can even add a prefix to each of your sequences for each of your manual stores.
To set up your manual orders to have order numbers assigned to them automatically.
Head to your Account Settings (the wrench icon in the upper right).
Next, select Selling Channels and then Store Setup from the sidebar on the left.
Select Connection under the "Actions" header for your ShipStation manual store. Alternatively, you could create a new manual store, if you wish to leave your original manual store the way that it is.
You'll then be presented with the choice to have your orders for that store automatically numbered. You can also set up a prefix to identify this store over your other manual stores, if you wish.
To set up automatically numbering your orders, simply check the box next to "Automatically generate order numbers to new manual orders", and input your starting number in the highlighted box.
Now, whenever you create a new order for that store, you'll see that the order # field is automatically populated. Just in case, you do have the option to set your own order # by unchecking the box next to Auto.
If you import any orders via a CSV file, and you want them to auto number themselves, make sure to put "AUTO" in the Order # field in the spreadsheet.