Any time you have a pop-up menu (a disc menu that is overlayed onto the video) with sound effects, those are secondary audio. Also some bonus features use secondary audio, such as commentaries and trivia features that can be viewed on top of the main feature. The most notable example I've run into is HBO's The Pacific, which has a lot of bonus material available separately from the main feature that uses secondary audio. Because the bonuses can be viewed in-line with the main feature as well as separately, all the bonus audio is set up as secondary audio.

As a general rule, bass management is handled in the digital domain. Stereo analog inputs are converted to digital typically, so we can apply surround processing and room correction as well as bass management, although most processors offer an "analog bypass" mode that can be selected to leave the stereo inputs analog all the way through the processor (which means no room correction or bass management). Multichannel analog inputs are handled in a variety of ways. The most common is a purely analog pass-through, with the processor only providing volume control. In some cases, analog bass management can be applied to the multichannel analog input (the Model 950 and Model 970/1070 being prominent examples of this). In other cases, the multichannel analog input is converted to digital for bass management. The Model 990 does this (as do the Sherwood R-965 and P-965 that the Model 990 was derived from), and I think some of Anthem's processors have done this as well.