Profile Manager - Custom settings

[petben]

I am trying to set software settings using plists deployed through the 'custom settings' bit of profile manager Yosemite

 

They are being applied to the Mac clients, but Profile manager seems to be putting the plists here:

/Library/Managed Preferences/'username'

 

 

but all the software to be configured wants them here....

/Users/'username'/Library/Preferences

 

any ideas?

thanks