Use call
to run a batch script in your current context - that is to have any environment variables set their values in the parent context. ie:
@call "%VSCOMNTOOLS%\SetEnv.cmd"
Edit
Here is how I actually setup the compiler environment in one of our build scripts. We have a chunk of code that sets PF to the 32 bit program files path for the current system. Then call vcvars32.bat to configure the compiler environment. If SetEnv.cmd is not working for you, using vcvars is likely to be ok.
@rem Note: can use @call "%VS120COMNTOOLS%\..\..\VC\bin\vcvars32.bat"
if "%VCINSTALLDIR%"=="" call "%PF%\Microsoft Visual Studio 12.0\VC\bin\vcvars32.bat"