Compiling and linking are controlled by the cobol command and cbllink utility respectively, both of which operate in Visual COBOL Build Tools for Windows in exactly the same way as they do in Visual COBOL.
See Compiling from the Command Line and Linking from the Command Line for full information on how to use the cobol command and cbllink utility to compile and link your COBOL applications.
If you need to set Compiler directives that in Visual COBOL you would have set from the IDE you will need to specify those in a alternative way. The different ways in which you can set Compiler directives are described in Setting Directives Outside the IDE.