best way to cook beans from dry?

this seems like cooking 101, but I have a real issue with cooking beans it would seem.

I've bought good beans (Rancho Gordo), soaked them overnight in cold water in the fridge, and tried my darndest to bring them just to a boil and then turn them down to barely a simmer so as not to agitate them and have them burst/skins crack. I'm cooking mostly in just water, sometimes with some carrot or onion thrown in, never salt until the very end.

can anyone tell me what I'm doing wrong? or am I just not meant to cook beans??

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