You absolutely can, just be aware that if you start mixing versions of components (jquery, jquery ui) that are different than what your version of JuiceUI ships with, we can't guarantee the results. If you do this and have issues moving forward, please remember to mention what versions of the scripts you're redirecting juice to use.
Check out this line here:
https://github.com/appendto/juiceui/blob/master/Juice/JuiceApp.cs#L25You'll want to add the same code in your application, effectively overwriting the keys previously defined.