I'm assuming it's just going to play back the MKV files as one long song. Some people here create .cue files with MMHelperCorrect, the Atom 4K plays MKV files that contain Atmos audio. The Atom 4K connects by HDMI to my Denon AVR which then plays that Atmos audio over all 7.1.4 channels. You must use HDMI between the Atom and the AVR.
The Atmos 4K does seem to accept USB 3.0 drives. I am using a portable SSD drive over USB 3.0 and it works fine.
Like you, I use a separate method for playing non-Atmos multichannel audio (5.1 MP4, FLAC). I put those files on a USB stick connected to my Sony X800 Blu-Ray player, which is then connected to my Denon AVR.
If, at some point in future, the Atom 4K supports MP4 and FLAC 5.1 audio, I can use the Atom for all of them. However, I contacted Neumi about this and they said that to enable support for those other formats would require a "new chip". Therefore, it is unlikely the current release of the Atom 4K will be upgradeable (i.e. firmware update) to support that.
to let them play back the file as songs. Have you tried that?