You only index titles and terms like Jr, Sr, III, when there is a field titled Suffixes or Title and Terms. Usually the field helps for the given and surnames will have some instruction like: Do not include titles or terms, such as "infant" or "Jr," with the name. Do not correct misspellings or expand abbreviations.
Field helps are accessed by clicking on the purple question mark that appears when you click on the fields. They always provide a great deal more information in addition to the project instructions.