Intelligent design. Philosophy of ignorance.

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when Theists are accused of filling the gaps left by science with God. Aren't Atheists doing the same thing when they pass off the gaps in science as something scientists just haven't figured out yet?

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You forgot part of the sentence:The gaps in scientific knowledge are things that scientists just haven't figured out yet and may never figure out.It is quite probable that there will always be gaps in our knowledge of the natural world.

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When we say we don't know the answer then the answer could be God or it could be we just haven't found it yet.

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So, how do you tell the difference between a natural system that we don't understand yet, or one that we will never understand, and a system that God designed?

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However, regardless of one's opinion the search should continue.

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But if someone concludes, "godidit", why should the search continue?

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I think though, that if we consider things like why we exist,

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If you mean, "What is the purpose of our existence in an existential sense", then no, science will not find an answer to that question, because it is not designed to answer such a question.It is as nonsensical as expecting science to discover if an action is right or wrong.

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why do we have a moral code,

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Science already has discovered quite a lot about why we have a moral code, through human research and also through work done in other primates.Put very simply, we have moral codes because we are social animals, and having moral codes makes it easier to live together in relative harmony.

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or even why does the universe exist, it is reasonable to conclude that science is not likely to find the answer.

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Again, if you are expecting science to give you an existential-type answer to the purpose of the existence of the universe, that is simply unreasonable.

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In my view, although many here aren't going to agree, an intelligent designer is the more logical non-scientific conclusion to come to.

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Where is it written that the universe must provide you with an answer to any question?Why do you feel entitled to know the purpose of existence?What is so frightening about saying "I don't know" and leaving it at that?

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What I really hear her saying is that the only way we can find truth is through the scientific method. I am all for using the scientific method to find out anything that we can but I believe that we can also gain knowledge through the non-scientific.

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How?

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I think most of us would agree that love is good and hate is bad.

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"Good" and "bad" are completely relative terms and are dependent upon the individual situations in which they are invoked.They are meaningless terms in the general. They are useful only when defined, and the definitions have and will always change in infinite ways.

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It's something we take for granted but I don't believe that we will ever find out why we feel that way using the empirical method.

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Let us assume for a moment that you are correct.Why do you think any answer that is not derived from methodological naturalism is going to be reliable?If it isn't testable, then there is no way to determine how close to the truth it is. If you aren't using MN, in other words, all explanations are equally valid.But I do not assume that you are correct.If our feelings of "love" and "hate" are products of the mind, which is in turn a product of the brain, there is no particular reason that MN won't be able to understand it in the future.We've only been really studying the brain as the organ that produces the mind, in earnest, since the 1980's, since PET scans were put into use at that time. Before that, there was research starting in the 1960's that used brain damaged people to dtudy behavir, and a few tests were done during brain surgery.So don't you think it is rather premature for you to poo-poo the possibility of science figuring out where "love" and "hate" come from, and why we think either are "good" or "bad", considering that the study of the brain has only really been going on for 40 years of so?