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}
You could also keep the document page sizes by adding a option:
\includepdf[pages=-,fitpaper]{paper1}
\includepdf[pages=-,fitpaper]{paper2}
And not to repeat yourself use this:
\includepdfset{pages=-,fitpaper}
\includepdf{paper1}
\includepdf{paper2}
\includepdf{paper3}
\includepdf[fitpaper=false]{paper4} // you can add document specific options
\includepdf{paper5}
\includepdf{paper6}
\includepdfset{} // to put default values back
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 to pdftk
.
$ 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
qpdf
is a command-line tool and C++ library that performs content-preserving transformations on PDF files.
$ qpdf --empty --pages file1.pdf file2.pdf -- output.pdf
GUI
This question is very similar although the questioner didn't realize it.