EasyApache / MultiPHP and addon domains outside public_html

cPanel 80.0.13, I have several addon domains configured with their document root located at ~/domains//public_html. The primary domain on the account points to the standard ~/public_html. This allows me to nicely organize all of my domains, and to have a clean and easily understood directory structure. When I go into the MultiPHP INI Editor, or the MultiPHP Manager, the only domain listed is the account primary domain. How can I go about managing the PHP settings for my addon domains with my current configuration? Also, perhaps this is something new (new server, and haven't used cPanel in about a year), but all of my error logs are going to the wrong place. I'm used to them being placed in the same directory as the offending script that raised or threw the error in the first place. Now the only place I can retrieve my error logs is ~/logs/.error.log. Is this expected behavior? Is there a way I can get my traditional same-directory error logs back?