When you installed the NonStop cross compiler, there should have been included an HTML document named UsingCommandLineCrossCompilers.htm, or something similar to that. Its first few sections contains the information needed for setting up your environment to use the cross compilers. Most of the rest of it are details needed only when using the Eclipse-based development environment or using embedded SQL in your programs, but the first few sections probably would be helpful for you.
The main things needed to be set up to use the cross compiler from the Windows command line are setting COMP_ROOT and PATH:
set COMP_ROOT=<Install-Dir>\HP NonStop\H06.nn
path %PATH%;%COMP_ROOT%\usr\bin
The H06.nn should be the exact release ID of the version of the cross compiler you installed. The cross compiler name is c89. There might also be a c99 included in more recent releases (I don't know whether they include that in the cross compilers).
You probably will have to modify the flags your make file passes to the c89 compiler if you use any that are not supported by c89. Check the flags you use against the documentation for the NonStop C/C++ compiler to find whether they mean the same as they do with GCC. You can get a list of the compiler flags by using the command c89 -Whelp but that gives only the syntax. If you want an explanation of the meaning of the flags, you can either look at the man page for c89 (or c99) in the OSS environment on your NonStop system, or look in the online manuals for the OSS Shell and Utilities manual (go to
www.hpe.com/info/nonstop-docs, choose your NonStop software release, then search for that title).
You might have to include the flag –Wtarget=tns/e if you want to run your program on an Itanium-based NonStop system. If you will be running on a NonStop X system, that might be –Wtarget=tns/x (my copy of the document precedes the NonStop X, so I don't know for sure how it is designated). It might be that the default for target in your version of the cross compiler does match the system type you will be using, and if so, you will not need this flag.
If you want to run your program in the Guardian environment rather than the OSS environment, you will need the flag -Wsystype="guardian"