As
Richard MacCutchan[
^] mentioned in the comment to the question, you can place it whenever you want. It depends on the menthod you wrote a script.
If you wrote a script as follow:
rem this script should be placed inside the main directory of solution
set buildtool=%windir%\Microsoft.NET\Framework\v3.5\MSBuild.exe
set solution=theNameOfYourSolution.sln
%buildtool% %solution% /p:Configuration=Debug
%buildtool% %solution% /p:Configuration=Release
you have to place it in the main directory of solution.