How was this done....

At the website....

http://www.ascensionlatorre.com/philosophy

....notice the pictures in the background and how they seem to move in layers, how was this done?

http://www.chris-wang.com/

....the navigation seems to fill up in color, how was this done?

 

Both done using Javascript namely implementing Scrollto

The Moving backgrounds is similar to this http://www.ndoherty.biz/demos/coda-slider/2.0/#4
You just need to tweak it to your needs and this will work.

The Menus are also done using the JS codes implemented with the CSS. As the functions are applied using the hover/mouseOver states to create the effects.

 

This can also be done in Flash by setting each photo layer to move in at independent speeds.

 

It was done in javacsript, when it should have been done in CSS...and just for the fact that the top banner seems like a separate frame from the content area makes me dissapointed at the site. It's 2012, what are people still doing using what can be confused for frames?

 

At a glance, the top looks like a creative use of CSS and Divs hidden and showing, and the second site looks at a glance like its using Divs and very possibly AJAX