I think I got it right.
Create a new ccs project with no main.c
Copy the contents of the zip file into the project, overwriting any existing files.
Copy usbhhid.h into the appropriate directory
If your project has the startup_ccs.c and a tm4c1294ncpdt_ccs.c exclude the tm4c1294ncpdt_ccs.c from the build.
*The naming could be different, but if you have two startup files you will probably get three re-declarations. At any rate exclude the one that CCS generated from the build and use the one from the zip.