Repro

gistfile1.txt

First, create a plist file with the keys you want to manage.
defaults write my.great.app setting1 -string foobar
defaults write my.great.app setting2 -bool false
defaults read my.great.app
{
    setting1 = foobar;
    setting2 = 0;
}

mcxToProfile to create a Profile to manage the domain "often".
mcxToProfile.py --plist ~/Library/Preferences/my.great.app.plist --identifier MyGreatApp --manage Often

Setup an unmanaged test VM or use a test machine running Yosemite. 
Copy the profile to the test machine and install it

sudo profiles -IF MyGreatApp.mobileconfig

You can see the preferences have been applied by running
`defaults read my.great.app`

Add some custom preferences after the Profile was installed:

defaults write my.great.app setting3 -string Chickens
defaults write my.great.app setting4 -int 42
defaults read my.great.app
{
    setting1 = foobar;
    setting2 = 0;
    setting3 = Chickens;
    setting4 = 42;
}


Log out and back into OS X and read the plist again.
defaults read my.great.app
{
    setting1 = foobar;
    setting2 = 0;
}