You just point it to the source code (C or C++ only) or executable, punch in the test case folder, and give it the time frame it's supposed to run in.
If you need to evaluate something more complex (i.e. with more than one solution or with special formatting), you can use the -e option to specify another source file or executable that should return 0 if the input (stdin) is correct or non-zero if it's not.