Hi Ryan,
Welcome to the forum. You’re asking a really good question here—when I first started tackling the subject of science and faith seriously I had exactly the same question. There are two things that I eventually figured out were causing a lot of my confusion, so I’ll give you the answers that made sense to me. Hopefully they’ll make some sort of sense to you too.
The first thing that causes confusion is the term “Intelligent Design” itself. It’s quite understandable that when you hear this particular term, you’ll think that it refers to the general belief that “in the beginning, God created the heavens and the earth.” In actual fact, it doesn’t refer to that general belief at all, but to a specific expression of that belief by a specific group of people with a specific agenda.
The stated objective of Intelligent Design is to try to come up with a rigorous scientific basis for demonstrating conscious and intentional design in nature. The problem is that ID supporters frequently make premature claims that are often subsequently shown to be incorrect—for example, the bacterial flagellum has been shown not to be irreducibly complex as they claim after all. They also tend to come out with a lot of rhetoric and insults, especially against “Darwinism.” That in itself sounds like it means something specific, but the definition is in reality so vague and ambiguous that it often results in their supporters being misled about what they actually believe about evolution. I have friends who thought that the Scientific Dissent from Darwinism was in support of a young earth, when in actual fact, most of its signatories acknowledge the vast age of the earth and the universe, and some of them even acknowledge universal common ancestry of humans, animals and all life on earth.
The second thing that causes confusion is the way that Intelligent Design is often attacked as being “religion, not science” or “introducing religious presuppositions into science.” This in particular caused me a lot of confusion because I frequently saw other Christians making this argument as well, and it made me wonder what they were doing apparently promoting atheism.
For my own part, I strongly recommend that people avoid raising this objection. Besides completely missing the point, it’s a very US-centric argument that is all tied up with culture wars about what exactly the First Amendment is supposed to mean. The US Constitution may be one of the greatest literary achievements of all time, but it is not a part of the Bible, it is not the ultimate authority on what is real and what isn’t, and for those of us living on the other side of The Pond™, it is completely irrelevant. Instead, I recommend that ID critics stick to insisting that ID proponents make sure that their claims are accurate and up to date, and to insisting that they come clean to their supporters about exactly which aspects of the theory of evolution they are rejecting and which ones they are not.