How you organize these items would largely depend on your internal processes and workflow. One solution would be to draw the alternates as regular constructs and then create special views for them.
If you want to present completely different plans/elevations to represent Alternates, you could use divisions to represent them; when generating the view, you just need to include the appropriate division into the view.
In some cases you might also consider copying the project and putting the Alternates into the copied project. If you copy a project, however, you have 2 different file sets to maintain; the copied project does not retain any links to the original one.