I never shipped any, but had many bikes shipped to me. Not ebikes, but the DH bikes that I am building on.
They all came in standard bicycle boxes, identified as such. The only parts removed were wheels, pedals, handlebar and fork. On most, the headset was left in the head tube tied with a tie wrap, in order to make the re-installation of the fork quick and easy. The axles were put back in place after the wheels had been removed. A double cardboard spacing sheet was between the bike and the parts that were bubble wrapped. Some boxes were filled with foam peanuts. I believe there is a flat rate to ship a bicycle standard box, but an ebike being heavier, some additional fees might apply.
The batteries should be shipped separately according to regulations for packaging and warning stickers. If you leave them with the bike, it will be at your own risk.