Jared,
when creating a project, in the second step, you will see a button as "Set
options". In the "Experts only" tab change the option under "Rewrite links:
internal / extarnal" to "Orginal URL / Original URL". 

Relative is dotted paths as you now see. 

Absolute is the path beginning from the root (like "C:\Users\user\Desktop\.."
in Windows or "/home/user/Desktop/.." in Linux).