Hello Alexander,
Congratulations for successfully porting Cornerstone to cm 10.1. We have archived your link to Cornerstone github wiki page:
The issues you are describing are most likely layout issues and I suggest you go through carefully to layout customization page:
Note that for better layout as per your screen size, you also have to make changes in Cornerstone Panel app layout files. Please go thorough the above wiki for detailed info.
For rendering only two windows (1 Cornerstone Panel + 1 Main Panel) than 3 windows (2 Cornerstone Panels + 1 Main Panel), you have to review the code into ActivityManagerService and WindowManagerService classes. Of course, you do have to modify the Cornerstone Panel app layout files and CSPanel.java class as well. This would be the starting point if you want to modify the number of windows rendering on whole screen within Cornerstone.
Also let us know the device you are testing. Is it Huawei Media Pad 10 FHD?
Let us know if above info helps you.
Thanks for using Cornerstone.
Sanjay Jain