I have an directory called /patterns in my Jekyll site, whose structure generally looks generally like this:
_includes
_layouts
_site
/patterns
index
You can change the directory that the include tag uses with includes_dir in your _config.yml. It doesn't look like you can set multiple paths (source: https://jekyllrb.com/docs/configuration/).
In any case, the files in _includes don't end up in your output. You could separate pattern-specific includes into _includes/patterns/, but the only thing that'd have any effect on your live site would be where those files were included.