I have some specific programming questions like what command should be used in a certain situation or questions like how do I do X with Y. Which Stack website would be the best? I am thinking http://programmers.stackexchange.com/.
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Your example question (How do I do X with Y) sounds like you are seeking code-specific help, so that would be more appropriate to post on Stack Overflow
If you were asking for more conceptual code help, than Programmers would be more appropriate.
To quote from the Programmer's meta post about the difference between StackOverflow and Programmers: