The problem you have is---if I understand your question right---that you need to process more than one index file.
The general way in your case is (let's say you code is in file
pdflatex mwe.tex. No check the directory of this file. There you will find several files
*.idx, depending on your code you did not show us.
- Now you have to run
makeindex with each of the created
idx files. To do that in one run write an batch file and add there all
makeindex runs you need.
- In the relevant TeXniccenter output profile add the batch file
mybatch.bat into the postprocessor. Then, if you compile your
mwe.tex file is the batch file automatic run afterwards, so that with the next compile run(s) you will see the resulting indices in your document.
Example for the batch file
makeindex name.idx -t name.ilg -o name.ind -s nomencl.ist
makeindex place.idx -t place-ilg -o place.ind -s nomencl.ist
Add more lines if needed. Change the names
place as needed. If you have an own index style or several styles change
-s nomencl.ist to the right style file name.
If you show us a complete MWE I can show you the screenshots for the configuration you need for TeXnicCenter 2.0 stable.