It's really based on media type per which black is used. If a media type works on the opposite black setting, but you want to change which black is used, use the MCT (Media Configuration Tool) to create that media type and switch the black. If you haven't downloaded the MCT, it's free off Canon's site.
All cartridges will go through the cleaning process since they each have separate lines to the head.
Technically, anything that has no sheen will use the Matte Black and with a sheen uses Photo. If you print on the Smooth Pearl, it will use Photo Black. But again, you can change the setting if the other black works better on the media type by creating a new media type from the MCT.