If you are using CCSv5 to build makefile based projects such as embedded Linux / u-boot spl etc, then you will likely get error boxes and if you want to use an emulator e.g SD 560 forget it. The basic CCSv5.2 to CCSv5.3 update does not update CDT.
I upgraded to the latest CDT tools (Version: 6.0.0.201211091924) using Help->Install New Software->Available Software Sites, Select CDT and follow normal process.
Oh if you get dependance issues, it may well be the help system which you can simply deselect.
Back up and running building native CCS and Makefile projects. :)