Let's say I find a question which is similar to one I already have, but I don't understand the answer, even though the OP got it.
What's the best way to ask my question?
e.g. Should I post a reply to the other thread, make a new question but link to the other thread, comment, or anything else?
That depends on what you don't understand - the answer on that question is pretty comprehensive (and anything that's not covered could be better answered by Wikipedia (or this one, or this one).
Generally the best thing to do is to ask a new question (with enough detail that it can stand on its own), make reference to the previous question, and explain why your question is different.
You can also pop into Server Fault's chat room for quick clarification (anything requiring in-depth explanation is probably better asked on the main site though, where more people will see it and benefit from it in the future).
