The layout you are referring is another layout.
It is not so simple to transform your layout to what you want.
I mean it is simple if you work on that direction.
You see, if you just make the navigation sidebar height as viewport height minus the header height, when the content of your page becomes larger than the viewport height, then the navigation bar will be sliding up as you scroll down, so it will not cover the whole viewport height again... You should go for a position-fixed solution for your sidebar and then adjust the rest content of your page with a margin-left
I suppose you can take a look at this
or just search in here and you will find usefull tips