We learn the On’Yomi first and Kun’Yomi 2nd. The mnemonic stories for each one are usually unrelated (not always), but when they are related it’s easier to remember them, especially if the On’Yomi mnemonic comes first in the story.
Examples:
Wait is たい and ま and the mnemonics are a man loitering outside a temple adjusting his tie, and you waiting for your ma. How about the man is waiting for his ma? Roll them into one, but also keep the On’Yomi mnemonic first in the story and the Kun’Yomi mnemonic 2nd, that way you can easily remember which is which.
More good examples:
Walk is ほ and ある, The story could be that you step on the hoe, it hits your eye, then you talk like a one-eyed pirate.
Another obvious example, the breath mnemonics are: you inhale a そく and you smell someone’s いき breath, these could easily be one story where the sock comes first and then the icky smell comes 2nd.