I am confused as to where or if I should put Jr or Sr in which section. I know it is not a prefix.
Unless there is a Suffix field, we do not index suffixes.
Check the Field Helps for Given Name and Surname. They should indicate if for some reason a suffix or prefix would be included.
For example, from, "US, Virginia—Vital Records, 1715–1901"
Principal's Given Name: "Do not include titles, terms, prefixes, or suffixes with the name."
Some surname helps state to index the surname exactly as written. There is a suffix after the surname. Do we include the suffix with the surname?
No do not include the suffix. IMO a suffix is never considered as a surname. So the statement "index the surname exactly as written" does not contemplate indexing a suffix unless there is a suffix field.
@Chas Howell is correct. Suffixes are not considered part of the surname and I can only recall maybe three projects that I've done in 7 years that had a suffix field.