Is it natural to really struggle to remember the onyomi

For now I recommend to focus on Kanji and maybe Grammar in a few levels. Once you’re around level 10 and want to start reading you can use things like Jalup, KameSame, Anki Core decks, Torii. You can also try to read things and specifically learn (via Anki, e.g.) the words that you didn’t know in those texts.
But for now, you really shouldn’t worry about vocab yet.