What happens to the default query when I use WP_Query?

WordPress always queries a default set of posts when you view any sort of archive. So if you run your own query as described you’ll end up with 3 database queries instead of 1.

You should not develop your template the way you describe. The standard WordPress templates should all use the default query. You’ll be coming back as the 400th person to ask why pagination isn’t working properly if you do it this way, among other potential issues. If you want to style the first post differently there are plenty of ways to do that without querying it separately, from CSS techniques to logic in the template. If you have something specific you’re trying to accomplish, I suggest posting a new question with those details.