You can add comments to a VI that you are checking in. This is done under SCC Check Files In >> File Properties >> SCC Edit Change Comments. If you want to see all comments go to SCC Advanced >> Select your project >> Select a VI >> File History. You can add a label to a version of a VI from the SCC View File History window. Click the 'Label Current....' button and add a descriptive 8 character name.
2. You can create a 'Project Group' for projects that you want grouped together. I cannot see a way to group specific files together based on a their labels.