FileMaker can not merge two generated PDFs into a single PDF file.
It CAN append pages to an existing PDF using the save records as PDF command. So if you have a container based PDF, you would only be able to add pages on the end of that, but NOT merge the PDF from the container field onto the end of a PDF you created earlier.
However, by augmenting filemaker with a plugin, it may be possible to create a merge feature that will merge two generated PDFs into a single file. Here's a topic I found on the subject using the free 360Works scriptmaster plugin:
This may also be helpful:
You can MBS Plugin.
PDFKit functions for Mac only or DynaPDF functions for cross platform PDF editing.
Good links, Matt's code uses quite an old version of the library, but there is updated functions at fmforums.com in the ScriptMaster section. Used with iText, the fastest way to do the job.