Merge two PDF files output by LaTeX?
Create the separate documents separately and merge them with a PDF utility. Semantically speaking, I feel this is the way to go rather than futzing with the document settings. After all, what you are submitting is not one "document" but a set of them.
Edit: This is an important question that has been asked more than once. It's also not exactly TeX-related. So I'm community-wikifying my answer so it can be improved and made definitive.
LaTeX
use Herbert's answer: the pdfpages package
\documentclass{article}% or something else
\usepackage{pdfpages}
\begin{document}
\includepdf[pages=-]{paper1}
\includepdf[pages=-]{paper2}
\end{document}
Command Line
pdftk
$ pdftk 1.pdf 2.pdf 3.pdf cat output 123.pdf
GhostScript
$ gs -q -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=merged.pdf source1.pdf source2.pdf source3.pdf etc.pdf
(via Macworld)
PDFJAM is a suite of scripts that uses LaTeX and pdfpages on the backend.
$ pdfjoin foo1.pdf foo2.pdf --outfile bar.pdf
(via Uwe Hermann)
stapler
is a pure Python alternative topdftk
.$ stapler cat in1.pdf in2.pdf out.pdf
PyMuPDF is a Python binding for MuPDF – “a lightweight PDF and XPS viewer”.
$ python -m fitz join -o output.pdf file1.pdf file2.pdf
GUI
Preview (Mac only) example
Acrobat Pro (non-free) video example
GUIPDFTK
PDFCreator (Win only, free, Open Source, acts like a printer ⇒ no hyperlinks etc.)
PDF Mod (Linux, free software)
PDF-Shuffler (Linux, free software)
PDFsam (JRE - Windows, Linux, Mac, free and non-free versions)
This question is very similar although the questioner didn't realize it.
Package pdfpages
may help
\documentclass{article}% or something else
\usepackage{pdfpages}
\begin{document}
\includepdf[pages=...]{paper1}
\includepdf[pages=...]{paper2}
\end{document}
If you have Ghostscript installed, you might also join the two separate PDF files in one by issuing a command such as this:
gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=merged.pdf input1.pdf input2.pdf