Where store a lot of arrays?

Both. Use separate configuration files to put your data and then create a library (it could be a model too, $this conveniently behaves there in a similar way as in controllers) that is to read the configuration files within their methods or, if necessary within the constructor. While reading this specific configuration use the "section" parameter for not making a possible conflict with the existing common configuration. Then in your application use only the library (or the model), it will "know" where to read data from, writing code would be easy.