To answer Q1, imagine you have master.tex, indiv1.tex and indiv2.tex. The challenge is to typeset master.tex, which includes indiv1.tex and indiv2.tex (with a bibliography) and to typeset indiv1.tex and indiv2.tex separately, also with a bibliography. The bibliography file is named "biblio.bib".
To solve the problem, create a single file named preamble.tex that each of master.tex, indiv1.tex, and indiv2.tex will include. In preamble put the following, which configures your bibliography and creates a command to conditionally include it:
%% Using biblatex to define the bibliograph.
\usepackage[natbib=true,style=authoryear,backend=bibtex8]{biblatex}
\addbibresource{biblio.bib}
% Used by included files to know they
% are NOT standalone
\usepackage{ifthen}
\newboolean{standaloneFlag}
\setboolean{standaloneFlag}{true}
%% Command to conditionally typeset a bibliography.
\newcommand{\standaloneBib}{%%
\ifthenelse{\boolean{standaloneFlag}}%%
{\printbibliography}{}}
Change indiv1.tex and indiv2.tex to start with the following header and end with the \standaloneBib command:
\documentclass[12pt]{report}
\usepackage{standalone}
\input{preamble}
\begin{document}
...
\standaloneBib
\end{document}
However, in master.tex, you set the standaloneFlag value to false, \input the individual files, and always print the bibliography:
\documentclass[12pt]{report}
\usepackage{standalone}
\input{preamble}
\begin{document}
\setboolean{standaloneFlag}{false}
...
\input{indiv1}
\input{indiv2}
...
\printbibliography
\end{document}
Now you can run pdflatex on indiv1 or indiv2 and only that chapter will be typeset, with a bibliography. If you run pdflatex on master, it will typeset all chapters, including the bibliography.
standalonepackage, and personally don't see anything wrong with compile vs typeset. – Peter Grill Jan 19 '12 at 19:19