Tolerance stacks are common sense issues to determine if all the parts of your mechanism fit together, allowing a functional mechanism without being overly costly (too tight of tolerance on parts). If you can do simple arithmatic, then you can do tolerance stacks.
I have found, though, that many engineers and designers can not do this simple arithmatic. Someone who can do 3rd grade math is portraid as the department guru.
All tolerance analysis needs is time, a trusty calculator, and a focus on what the final (functional) design requirements are.
As zzy stated above, there are computer programs that do tolerance stack-up, but for the most part this technology in relation to CAD is in its infancy and rather cumbersome to use. You are better of doing it long hand.
If you have a specific example that can be described here, I'd be happy to walk you through one.
--Scott