In GoAnywhere you can specify multiple modules in a project. Some of these modules could be used for error processing while others can be used for organizing tasks. In the example below I have specified a project level variable called FirstOrSecond. If that variable is set to a 1 the "First" module will execute. If it is set to a 2 the "Second" module will execute.

When GoAnywhere executes this project by default it will begin with the Main module. On the Main module I've added a couple modules to the Depends On attribute which are separated by a comma. Since the Main module depends on First and Second to run it will then pass control to the First module. I added a Execute Only If condition on that module to say to run only when the variable is set to a 1. I've also added conditional logic to the Second module to run only if it's a 2.

In the example below the "First" module will execute because the variable is set to a 1. The "Second" module will be skipped and then the "Main" module will finish execution. For demonstration purposes each module only prints some static text.
With this in place I can easily override the project variable at run time (via GoAnywhere's scheduler, Execute Advanced screen, RUNPROJECT command, etc) and determine what tasks will be executed.