Being able to set per-device SSID and passwords per WLAN as overrides is on our roadmap and is in development. As an enhancement of top of that we plan to add the ability to read and use the local device settings for certain overrides to prevent overwriting local changes made to the device. This would work similarly to the "Auto-set from device" feature currently available for network settings.
Which cnPilot device line are you using? Home or Enterprise?
Please also check out this thread below to get an idea of what we are working on and provide any feedback if we're missing something.
http://community.cambiumnetworks.com/t5/cnMaestro/Configuring-cnPilot-R-using-cnMaestro/m-p/86074