It's not bad to use it, otherwise it wouldn't be there.
The purpose of the manual mode is so you can choose when you want the vehicle to upshift and downshift. On average, 3,000rpm upshifts are a good idea, but shift points depend on your mood and driving style. For example, if you want maximum acceleration (assuming you're floooring it), you'd go to redline on each shift. Or you can do some hard acceleration and upshift at 4K or 5K rpm's. It's really up to you, it's pretty hard to abuse an engine these days, especially a BMW I6.