Virtualization

You can give permissions while installation and then Check on Enforce Security Descriptors in the package.

This will give the permissions to the App-V as you want.

Hello,
Never heard of such thing being done, but , at times, an application needs permissions to folders in asset directory or registry, now u can do that in two ways.
1. Either write a prelaunch vbscript, that will check if the file or folder has rights or not. If not , then it uses,either setacl.exe or cacls.exe to set rights to it. but a piece of advice while writing script, do not forget to set 

<LOCAL_INTERACTION_ALLOWED>TRUE</LOCAL_INTERACTION_ALLOWED>

2. During monitoring phase, u can set explicit to folders or files, just as you set them on any other folder in windows 7 OS.

Hope this clears your doubt