The Presets tab should configure most of the options for you, leaving only some nagging details, such as where the finished product will go, as well as naming conventions for the output files. In the "Tools>Options>Output Files" tab, you can select the folder that your output files will go. Make sure that your target folder is in a drive with a lot of free space, as videos can take up a lot of space quickly. You can also define the naming conventions of your output files, which is especially useful if encoding an entire batch.
Users of Apple devices and QuickTime might want to make sure that the "MP4 File Extension" is set to "Always Use M4V" if they want to keep a video file's Chapters and AC3 audio.