After you clear a cup once, re-enter the cup and click the icon in the bottom right corner to swap partner decks. From there, click on a deckbox icon and turn on the manual duel option at the top.
Why you have to play by yourself? The team AI is pretty broken. specially Crow. You can sit sipping your afternoon tea while he won you the whole tourney ;)
Crow is completely broken. I didn't have a single match where Bora the Spear had anything less than 4000 Attack.
But Yugi's broken af too. He'll purposefully wipe the player side of the field to get your lp low enough for his skill, you might as well just run a deck of equip spells and traps to keep his monster on the field