CyanogenMod is freely available for all users but Cyanogen OS is released only in OEM devices tied up exclusively.
In simple terms Cyanogen OS is the commercial version of CyanogenMod.
Cyanogen OS or CyanogenMod is all about customization whether it be themes, system configuration, system visual layout or whatever you can think of.
Cyanogen gained popularity because of the only reason and that is Customization.
Now Cyanogen OS 12 has brought(if not it will bring in the upcoming releases) a unique theme customization in it's Cyanogen OS 12 Lollipop release which has been released for OnePlus One and Yu Yureka users recently.
Cyanogen Bytes is the new app themer that will bring you per app theme customization that will allow users to customize different applications with different themes.
Believe or not this will be real fun for those who really wants change in the look of their phones.
[Cyanogen Bytes - The app themer preview]