Tips on setting levels in Cubase AI 6?

First off, the two values you mention.

One is the Value that the fader is set to relative to 0dBFS. It will change when you move a fader, whether a signal is present or not.
The other is the value of the peak signal for that channel, it is a measurement of the largest signal level.

The Master Stereo Out Channel is clipping (signal is beyond 0dBFS). This is due to the “summing” of several channels (the drums) The more signals you combine the bigger the result will become.

To prevent this from happening you can do one of three things!

Turn down all the drum channels, turn down the master fader or both.