Hmmm, you should not need an extra subsite package _under_ the main subsite unless that is a specific organization you need for your application.
For theming all you need is to apply the themes correct styles and master template in the package parameters for the main subsite. In this case there is no need to create a descendant acs-subsite package type at all.
You only need a descendant package type if you want to modify the behavior.
In either case, there isn't any reason to put your content under a second subsite.
You can either
1) Edit the parameters in the Main Subsite to point to the resources in the appropriate theme location. This has always been the case, the theme packages are just a way to encapsulate the styles and master templates in one place.
2) Edit the parameters as mentioned in #1 and convert the main subsite to a descendant package type if you want to modify the behavior of the subsite. Every web site I work on now uses this technique since the default openacs UI for acs-subsite is less than ideal, and certainly is not specific enough to meet most custom applications requirements.