there are a few, but imo puzzle design is its own artform, and: It's Hard. but like many artforms, one of the best ways to get a sense of it is to look at existing art that inspires you
for specifically managing the logic of a puzzle though... i don't know exactly what you're looking for, but if you want like a state graph or something, that's usually gonna be done with bespoke tooling, because it would depend so heavily on your rules. or you could wing it with regular ol flowchart software