Multi order ship imports non-paypal payments such as checks and money orders seperately off the import menu. Key is you need to mark the orders as paid in ebay first, THEN use the import function off the menu to get non-paypal orders.
In your multiship settings you can have notification of printing the label automatically sent to the customer, also.
You can also add your logo and a short message from EDIT>SETTINGS.
It's worth noting that if you print all orders at once, all the labels get printed first and then all the packing lists.
You can also turn off the receipt and save yourself half a sticky label.
You can even override shipping to eCheck customers before the check clears by marking them paid in eBay first. If a customer has good feedback, and your items not real expensive it could be good for repeat sales.