Knowing from [`:help ale-python-pylint`](https://github.com/dense-analysis/ale/blob/06f57ca9733aab6e6b67015917fdfd4bf1c70c48/doc/ale-python.txt#L594) that we want to adjust `g:ale_python_pylint_options` to [include `--rcfile`](http://pylint.pycqa.org/en/latest/user_guide/run.html), I would drop

```vim
let g:ale_python_pylint_options = '--rcfile '.<filename>
```

in wherever the right place is for you. That could be wherever you configure ALE, if a single setting is right; or, it could be in an ftplugin (use `b:…`) if you need to change the name based on the specific file/project/whatever.