I've completed the rough drafts of many books in my years of writing. What typically happens is I put the finishing touches on the book, read through it once, then put it aside so I can work on the next book in the series. I'm now to the point that I actually need to prepare the book for an agent. So then I ask myself, now what? How do I go about fixing up the book when I know I have a ton of errors interspersed throughout the text? Here are a few tips I've learned while updating my own book.

Breathe and Separate: Before you even start editing your story, take a minute to breathe. Separate yourself from the book for a few days, weeks, or even a month or two if that's what you need. If you jump into it too quickly, the story will be too fresh in your head, and that means it'll be harder for you to find mistakes. You want to read it fresh. And you also want to convince yourself not to get overwhelmed. This is not a fast process, so pace yourself.
Change the formatting: If you have your text double-spaced, single space it. If you have it single-spaced, double space it. You'd be surprised how different your book looks when you do this, and it can help you catch more errors than if you look at it the same way you always have.
Print it Out: As with changing the format, printing the book out allows you to look at the story in a different medium. This can also help you find errors as you go through it.
Separate the Chapters: If your book is in one document, then save all the chapters as separate documents. As you read through, you can mark off what chapter you're on. I find that knowing I have to review 44 chapters is less daunting than having to read almost 400 pages.
Quick Read Through: Once you've had time to breathe, read through your book once without making any changes. If there are changes you want to make, write notes so you don't distract yourself from reading through. This will help you focus more on plot errors.
Pick a Topic: When you decide to edit your book, after the initial read, only choose one topic to edit. Maybe you're checking for continuity errors. Maybe you're looking for plot problems, or grammatical changes. Whatever it is, edit one topic at a time because otherwise you might find it way too overwhelming.
Color Coding: Color code different types of errors to help keep your edits organized. Use "blue" for continuity problems and "green" to identify when characters show up. Post it notes also help with this if you have a printed copy.

These are just a few tips you can use to start off editing your first draft. As you go through, you'll become more comfortable with the styles that work for you. If you have any additional suggestions, post them below!