What you see next to the Overlay sidebar, is a frame that opens your actual website. The website needs to load some resources (JS/CSS) from Piwik and access the Piwik API (index.php). That's why linking piwik.js and piwik.php is not enough.
Loading these URLs (JS, CSS and index.php) needs to be possible from the machine you are viewing Overlay on. If they are not available via the tracking URL, you need to tell Piwik about the location where it can load the resources and access the API.
Unfortunately, I cannot debug your setup since it's not public. I can only tell you that you need to tell Piwik about the location where <APIURL>index.php opens Piwik using setAPIUrl.
Having that said, the problem may be elsewhere. Overlay is launched when calling trackPageView. You push it to _paq before pusing the config method calls (e.g. setAPIUrl). I don't this works.
Loading these URLs (JS, CSS and index.php) needs to be possible from the machine you are viewing Overlay on. If they are not available via the tracking URL, you need to tell Piwik about the location where it can load the resources and access the API.
Unfortunately, I cannot debug your setup since it's not public. I can only tell you that you need to tell Piwik about the location where <APIURL>index.php opens Piwik using setAPIUrl.
Having that said, the problem may be elsewhere. Overlay is launched when calling trackPageView. You push it to _paq before pusing the config method calls (e.g. setAPIUrl). I don't this works.