I haven't used skrollr.js but you can take a look at other pages using paralax and fullpage such as http://www.saltaboombox.com.ar/ to take ideas or to see how they have done it.
The problem with fullpage and some paralax plugins is that when using fullpage.js you are not actually scrolling but changing the top
property of the site (or adding a css3 translade3d effect).
Anyway, I would recommend you to add the scripts between <head>
and </head>
. Fullpage operates over the body and the way to avoid problems is having all of the scripts in the header.