1) The Band/Frequency will be different in both configurations
2) The Hw. Supported Modes (you can use gn for 2.4GHz or ac for 5GHz) and Master Configuration will be different in both provisionings
Based on those provisioning rules will CAPsMAN send correct configuration to CAP interface.
Example:
/caps-man configuration
add channel.band=2ghz-onlyn channel.extension-channel=disabled country="czech republic" datapath.client-to-client-forwarding=yes datapath.local-forwarding=no distance=indoors guard-interval=any hide-ssid=no installation=indoor mode=ap name=CAP-WiFi-2.4
add channel.band=5ghz-onlyac channel.extension-channel=XX channel.skip-dfs-channels=yes country="czech republic" datapath.client-to-client-forwarding=yes datapath.local-forwarding=no distance=indoors guard-interval=any hide-ssid=no installation=indoor mode=ap name=CAP-WiFi-5
/caps-man provisioning
add action=create-dynamic-enabled hw-supported-modes=gn master-configuration=CAP-WiFi-2.4 name-format=prefix-identity name-prefix=CAP-2.4GHz
add action=create-dynamic-enabled hw-supported-modes=ac master-configuration=CAP-WiFi-5 name-format=prefix-identity name-prefix=CAP-5GHz
This file should answer your questions about CAPsMAN Dual Band CAP, see page page 37+:
https://mum.mikrotik.com/presentations/BR14/Uldis.pdf
(little outdated, November 2014, but still nice explaining)