There are only 2 Runes and 1 character per world. Forgotten Cemetery, Bloody Mansion and Mystic Ruins are the only worlds that have Runes and a character. In order to obtain the achievement 'Rune Goon' you need to complete the game with any character with all 6 Runes all in 1 run. If you die or forget one, you'll have to restart from the beginning. For the character achievements, you just need to collect them.

00:00 Runes 1 + 2 and Butternut Bro

02:58 Runes 3 + 4 and A Skeleton

05:43 Runes 5 + 6 and Ms Witch