I use a free App called Musicolet on my mobile, I have about 40-50Gb of music on it in MP3 or Flac formats. It will also run through Android Auto.
The Skoda onboard media system is pretty useless, USB can’t remember last track played and always starts from the same track, media keeps changing it’s default startup setting between Media, Radio, Bluetooth etc.
The Android Auto is also pretty poor, whether it’s connected by bluetooth or cable it will sometimes take minutes to establish a connection to the phone, sometimes it will play the music but with a blank screen and supposedly unable to connect!. Previous Ateca (and every other car before it including 2 Skoda Yeti’s) had much better systems, never had any problems with them, so much for progress!
Please excuse spelling/typos. Apart from being a clot it turns out I had one on my cerebellum that's now causing various problems!