When you produce a full-text search catalog (local file systems; not applicable to web-based searched), you can associate it with PDFs included in the collection being indexed (or at least with some of the entry-points PDFs).
In Acrobat, this can be done through File > Properties, Advanced Tab, Search Index field. This action has to be repeated when the PDFs are recreated.
With FrameMaker-to-Acrobat TimeSavers, you can specify the index to attach in PDF Settings, Search index (under External References).
(This applies to all PDFs distilled, so it makes sense only when distilling multiple files from the same project)
You may also attach the index to specific FrameMaker documents, using the