Hello,
First, what do you mean by same container??
Do you mean, you are creating a same folder in which 32 bit and 64 bit packages would be kept for deployment purposes??
These packages are quite intelligent and they would get installed only when they are find the right type of Operating System (32 bit /64 bit)
Again, I would recommend you to check this Articles when using installing SEP via GPO.
See Installing clients with Active Directory Group Policy Object.
See Uninstalling client software with Active Directory Group Policy Object.
Hope that helps!!