When I start to work on a new project, I first note down all the information I have. I am a big advocate for the use of prototyping software. Of course it is good to start with something simple like paper wireframes, because you can visualize your idea quickly. But if you want to apply changes and your prototype starts to include more than one page, paper wireframes are not really handy. After this (I call it brainstorming) phase, I start to work with clickable wireframes. Even with the main structure of your planned website (or application) it is sometimes hard to start your digital prototype. Looking at an empty screen can be very exhausting. But don’t force yourself to much, just start to apply the UI elements to the screen (every prototyping tool includes predefined UI elements). It doesn’t have to be perfect from the very beginning. Because (and this is the big difference between paper prototypes and clickable wireframes) you can change even fundamental features very easily.
A lot of prototyping tools I know include the feature to create customized masters and templates. That means you only have to design your navigation bar once for all your wireframes, because with generating a master or a template out of it you can use the UI design pattern again and again. Mostly a master pattern can be adjusted differently from wireframe to wireframe (which is usable for the bar at the bottom of your page, as wireframes are often different in their length). Template patterns are in a fixed position on every page (this is handy for the top of your pages, if it’s supposed to look exactly the same on every screen). Clickable wireframes are easily designed, because you can just start, without worrying about whether it is perfect right away.