I'm using TeXstudio 2.6.2 with MiKTeX-pdfTeX 2.9.4535 on Windows7.
I configured TeXstudio to store all output files in a separate directory.
It now looks like this:
-src
|_Report.tex
|_*.tex (all chapters)
|_Report.bib
-build
|_Report.pdf
|_Report.log
|_Report.bbl
|_*.aux
which is my desired structure.
My problems are
- There are many messages like "citation 'X' on page Y undefined. There's the error message "no file Report.bbl"
- the inbuilt pdf-viewer doesn't open (find?) Report.pdf
My configuration looks looks this:

How do I have to configure TeXstudio properly in order to solve these issues?
bibtex? – Sigur Jan 07 '14 at 13:51biblatex, do you use that package?biblatexpackage usesbiberas default bibliography backend, so runningbibtexwont help unless you've specifiedbackend=bibtex. – Torbjørn T. Jan 07 '14 at 14:12