The default location for the compiler and run-time system files:
NX:
C:\program files (x86)\Micro Focus\Net Express 5.1\base\bin
and
C:\program files (x86)\Micro Focus\Net Express 5.1\base\bin\WIN64
VC:
C:\program files (x86)\Micro Focus\Visual COBOL\bin
and
C:\program files (x86)\Micro Focus\Visual COBOL\bin64
I would recommend that you do not include these folders within your PATH or COBDIR settings at the system level. On the development computer when these products are launched it will read the correct product locations from the Registry and so should be set appropriately.
If you are running your compiled executables outside of the IDE either from a shortcut or a command prompt then I would recommend that you set the appropriate locations from within a .bat file before launching each one instead of setting it at the system level.
If you start a Net Express command prompt or a Visual COBOL command prompt and launch your application from there things should be setup automatically for you.
Just make sure that you don't start copying run-time files like cblrtss.dll or cblrtsm.dll into your application directories or system directories as then they are prone to be picked up in error when the application starts. On the development system you should keep all of the COBOL components in their respective install folders only.