There may be another way to do it but I just include both items in with the package weight and dimensions. If it is an international transaction I change the customs form to show both items. I manually add the second item to the packing slip.
If the package has tracking, you will have to manually add the tracking information to one of the sales as it will show only show up on one of the purchases.
If both items are paid for together the above isn't necessary as both items should automatically show as being in one package.