In the bare-metal application, you accessed the registers of your PL kernels by computing the physical memory addresses. These memory addresses can change between builds and software releases. With the PetaLinux software platform, it is possible to bind general UIO drivers for each PL kernel instance. Instead of accessing specific physical addresses as you did in bare metal, use these UIO drivers which access the physical addresses for you.
Creating a PetaLinux application allows you to take advantage of a variety of other features such as security, multi-threading, and multi-processing.