Beginning writers often grumble about having to learn all this crap, but there's just no way around it. If you want a simple reason to pay attention to mechanics — even if you don't think it's a good reason — try this. People always judge you by the way you write, and that includes the little details. That may not be fair, but it's the way the world works. If you write “it's” instead of “its” or use a semicolon instead of a colon, your reader will probably know what you meant. But your reader will also think less of you for it. A fair reader will try to keep minor infractions in perspective, and pay more attention to bigger things, like your thesis. But (a) even fair readers are influenced a little bit, and (b) not all readers are scrupulously fair. You'll do yourself a favor by learning the rules as thoroughly as you can.
I'll eventually write more on this subject, but for now, my comments on mechanics are scattered throughout my Guide to Grammar and Style. See especially the entries on Block Quotations, Capitalization, Commas, Dashes, Ellipses, House Style, Hyphens, Justification, Mechanics, Paragraphs, Punctuation and Quotation Marks, Punctuation and Spaces, Semicolons, and Titles.
One new entry, though, is worth reading now: on typos and proofreading. That might tell you why all this stuff is worth caring about.