I capture all census images as PDF files. This gives me the ability to add notes to the census reports.
These comments may take different forms depending on what is needed. They vary from positional comments noting where the person is listed to explanation.
An example is my Knuttle family. In 1810 the family were living in Broome county NY, and after much work were found in the census. The Ancestry transcribers picked the name up as Thnuttle. I have added a comment to my copy of the census comparing the letters in Knuttle to other example of letters of other names on the same page.
NOTE: The Adobe Reader starting on version 10 added that ability to highlight and comment PDF files and resave the file with the comments and highlights. They can be removed or edited at a later date. So if your Adobe Reader does not have this ability you should upgrade.