To set or update the path to a software package like Nuke, Maya, or Photoshop, you need to locate the paths.yml file in your project's configuration. Your project configuration should have a structure that looks like this:
As you can see, the paths.yml file lives inside the includes directory within the config's top-level env directory. This file is used by Toolkit to identify the path to all of the project's software packages on the various operating systems in use. Each software package typically has 3 entries, one each for windows, linux, and mac. Here's an example of the default configuration for maya:
To change the path to a particular piece of software, locate the collection of paths that correspond to that package and update the path or paths for the operating systems in use. Save the file and Toolkit will use your updated path the next time you launch the software.
For reference, you can see the default state of the paths.yml file in the tk-config-default repository here.