For a front wheel, I might put the bike on its side, but for a rear wheel change I find it easier to get the wheel on and off with the bike upside-down. But then I generally don't have trouble turning the bike upside-down -- that's also how I clean and lube the chain.

If you do have it upside-down, make sure you get anything you need out of the bike bag(s) while it's still upright.