In the mixer, at the top of a couple of mixer slider travels are little red marks. On one channel there is one and on another channel there two. What do they signify and what is the difference between one and two marks?
Also, how can I clear them?
They are part of the Meter Animation…Individual or…Left…Right…Clipping/Peak=RED.
Just click on them to clear as is the case with the small ones on the right side of the Channel/Fader , you may have to click on the display in the Masters to clear…then adjust the gain/levels of kit piece(s)/Channel(s) etc.
If you don’t want Meter Animations you can go into Preferences…GUI and uncheck the “Animate” boxes…there are various Animations FX,Kit,Mixer for Hits…Meters.
The “itty bitty” (10) boxes to the right of each channel level display indicate when/if effect(s) are on…
I think they added a preference for clipping behavior (upon my request? 
). Also, you can set a shortcut key to clear clip indicators. I use the esc key.