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 https://softwareengineering.stackexchange.com/.
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:
In a nutshell, Stack Overflow is for when you’re front of your compiler or editor working through code issues. Programmers is for when you’re in front of a whiteboard working through higher level conceptual programming issues.
Stated another way, Stack Overflow questions almost all have actual source code in the questions or answers. It’s much rarer (though certainly OK) for a Programmers question to contain source code.