Do these settings have to survive power cycles or resets? If so, then I would probably go with something like SQLite3, or you could use MySQL.
If they don't have to survive, and only need to be remembered while the unit is powered up, then I might go with Bridge library Bridge.put()/get() calls, as much of the web interface is already there. However, these values will be lost on a reset.
Either way, I try to put as much of the "business" logic and processing on the Linux side (especially the web services - I use the Python Bottle framework, but there are many alternatives.) I try to keep the sketch simple and just do the I/O processing, and use the Process class to talk to the Linux side.