I have shipped many basses through eBay sales. All of my basses ship with a hardshell case. Some UPS stores sell a shipping guitar box that is just large enough to accomodate the bass guitar case; it sells for about $10.00.
I get one side of the box tapped up and then head to the local UPS store. I then put the bass guitar case in the box upright and then have them fill the box up with packing peanuts. You are correct, if you packed the box and there is shipment damage, they might not pay for a claim for shipment damage.
I then have them put "arrow up" and "fragile" stickers on all four sides of the box. Obviously during shipment, it will lay on its side but when they need to stack the box upright, it will be stacked correctly.
Make sure you tune down all the strings on the bass guitar until they flap loosely before putting it in the case. This will ensure that the strings will not break or that the neck will not get any undue tension. I also put bubble wrap around the headstock then use a rubber band to hold it in place. If the bass moves around in the case, I put extra padding in it to hold it in place.
I insure the bass and request that the delivery is signed for. When I get home, I email the tracking number to the buyer and then check on its progress daily until the bass has been delivered.