Don't ignore the submission guidelines, don't for example submit more than requested, explaining that the first 10,000 words didn't do your book justice and that you wanted to submit it differently. If that is the case - then you need to rexamine your first three chapters and really decide whether you are beginning your novel in the best place to really hook the reader and the agent. Take a look at our article here on refining the opening chapters of your novel for some tips.
If the literary agency guidelines state 10,000 words, submit ten thousand words. If the guidelines state the first three chapters, submit the first three chapters. Particularly don't expect the agent to read the entire manuscript, not at this stage.
Correctly formatting your submission is essential. See our formatting guide here
If you are submitting via email keep it simple. Arrange your submission letter, synopsis, manuscript sample pages and other material into one document before you start. Multiple attachments leave too much to go wrong at the receiving end. Remember a literary agent will receive many submissions each day.
Don't submit the first three chapters if you only have an outline for the remainder of your novel. If the agent likes your work, chances are, they will ask to see more pretty quickly. As a general rule, give yourself time to finish the book, put it away for a month or so and then come back to it for a final read and proofread before you start submitting.
Make sure you are submitting at the right time in your career. Are you absolutely happy that you have developed your writing skills sufficiently to judge that your manuscript is in the best shape possible. As soon as you submit your work to the literary world, you are setting yourself up for some harsh realities about your work - or not as the case may be!
Be prepared for rejection. Accept any constructive criticism on your book gracefully and use it to improve. Don't let rejection stop you - that may mean toughening up mentally before you start submitting. Try not to burn any bridges if you are rejected. It is a small industry and it is based on building solid personal relationships throughout. Don't tell an agent they have made a mistake if they reject you, books are rejected for many reasons and it may not be because yours isn't any good.