Configuration profiles are just xml documents that specify preferences. I found, when creating them on the JSS, that many more preferences were specified than I actually wanted to control. Basically, if you want to set one preference contained on a "page" of preferences, all of them get set. That is true if you create them in the JSS or upload them unless, as @Jedberg points out, they are signed before uploading.
If you don't need to use payload variables within your configuration profiles, which I believe are parsed, signed and delivered per device, I would suggest creating custom configuration profiles using Apple's Server application or hand-modifying them using a text editor. Sign them, and then upload them into your JSS infrastructure for delivering. This ensures that you won't start accidentally delivering configuration settings to your fleet that you weren't intending to. On the other hand, you are taking a degree of control over from the Casper Suite so you might not get added benefits as things change "automatically".
