Typically what I do is set a single parameter of "Tolerance" (not quite the correct expression, I know), and then gap it all to that parameter. That way, once I get a joint that prints properly and moves properly, I can tweak it up and down.
The details depend on the type of joint and what the movement type is. A ball joint you want to be able to support has different requirements than a hinge to support any weight.
Generally, I've found it much easier to design them for assembly than to print in situ after designing many hundreds of items that use joints in one way or another, unless it's a joint I want especially loose.