I've got a user that has used Ninite to setup his base apps on his PC. I want to use Chocolatey because it has some additional apps that I need and I can use it from the command line.
Do I have to start again with this PC, or can I run Chocolatey after Ninite?
You are fine to run both together, they essentially leave the same thing at the end in most cases, which is to work directly with the Windows Installer database (Programs and Features). You could even have one take over another if you are so inclined.