The first step is to be able to identify the presupposition, which is a claim that must be assumed to be true for the question to make sense. For instance, "Is the present king of France bald?" assumes that there is a present king of France, and that in fact is false. Such a blatant example is hard to miss (if you speak English), but a less obvious presupposition can be found in the question "When did you arrive at your subjective conclusion about the accused". Regardless of the time, answering the question accepts that the conclusion is subjective (not a god thing for an expert witness to be saying). If you want to study linguistic semantics, there are a number of ways to identify presuppositions: to keep it on topic for LSE, I'll just summarize it by saying you have to acquire the analytic skills for identifying presuppositions. The technical tests are probably not useful to a panicked witness being cross-examined. The Wiki on presupposition might be useful, for example pay attention to the negation test ("My car exploded" and "My car didn't explode" both presuppose that I have a car).
If you can identify the presupposition, you can simply answer "I have never beat my wife", or "My conclusion was based on objective scientific tests",
and ignore the literal question that was asked. They can still rephrase and ask an unloaded version of the question. If you are forced to limit responses to yes and no, you may need to address the judge to explain why you can't just say "yes" or "no", or blurt out the explanation before you are instructed to stop talking (the judge would probably allow the explanation if it's obvious that you're addressing a presupposition problem).