If you add manual <indexentry> markup to your Docbook XML then these will be passed through unchanged. Please note however, that if you are using AutoIndex's internal index generation then it only recognises <primary>, <secondary> and <tertiary> elements within the <indexterm>. <see> and <seealso> elements are not currently recognised and AutoIndex will emit a warning if these are used.

Likewise none of the attributes which can be applied to these elements are used when AutoIndex generates the index itself, with the exception of the <type> attribute.

For Quickbook users, there are some templates in auto_index_helpers.qbk that assist in adding manual entries without having to escape to Docbook.