The PDF Converter for SharePoint automatically converts (and merges) all files that are attached to an InfoPath form as long as they are part of the views that are being converted.
The conversion of attachments is enabled by default, but can be disabled globally using the Conversion Service's config file, or on a call-by-call basis when using the Web Services interface.
As it is not possible to merge different file types into MS-Word and Excel documents, attachments are ignored when converting InfoPath forms to file formats other than PDF.
All this behaviour can be tweaked. Store InfoPath attachments in the PDF as an attachment, rather than merging it into the main document, no problem
For more details see:
- Blog Post: Converting InfoPath attachments.
- Administration Guide (Search for InfoPath specific switches).
- Developer Guide (Search for ConverterSpecificSettings_InfoPath)
- Tweaking how attachments are handled.