Indexing a software manual is not very different from indexing any other manual. As a simple rule, make sure you index all of the software features: screens, windows, fields, options and commands. Index system errors and warnings if applicable. Use cross-references to direct the reader to the term used in the manual if it differs from the generally-used jargon.
Tetreault, Edouard. STC Proceedings (1993). Articles>Documentation>Indexing