If I'm understanding you correctly, you can do this with skrollr alone. Read the docs about relative mode https://github.com/Prinzhorn/skrollr#absolute-vs-relative-mode
Like this (you get the idea):
#logo.unit data-top="top:5px" data-200-top="top:-8px;"
Using data-anchor-target="#logo.unit"
you could even have the animation of other elements depend on the position of the logo.