You can vary the thickness by applying prepreg layers as you would do when building the composite layup in real life. One way is to create diifferent element sets for the regions where prepreg layers will be applied. Next, you create many Oriented Element Sets using the different Element Sets. Finally, you can add layers in different regions by selecting the appropriate Oriented Element Sets in Modeling Groups.
Another option is to use selection rules instead of Element Sets.
This is explained in the Ansys Composite PrePost course on the Ansys Learning Hub: