Reaper has a concept of stems, does Sonar have this same concept?  And if so, how do you tell Sonar to keep them in your projects folder structure?  I know this is probably a very basic question, but I'm drawing a blank here and when I went to the help file, it didn't seem to have any help on the word "stem"

A stem (submix) in Sonar would be a bus - i.e., all drums, snare toms, hats, o/h.. going to a bus. 

Stems as a concept is from the movies and video industry. Audio has used the term sub mix to mean the same thing. To create stems do as Super G says just export your buses and not the full mix. You want each buss to be a instrument group. 

Stems are nothing more than mixes that are further mixed or mastered. You could leave them in your project audio folder or export / copy+paste into a 'stem' folder either inside the project folder or elsewhere.