Then you just need to point to that file location for all future projects. By the way please post your current code so we can check it on our system. To do this please open Psoc Creator and select file and then select create_workspace_bundle. Then attach the Zip file you created to a new comment.
Okay I tried your program and it worked on my system. The AN54460 example is for PSOC 3 and PSOC 5 this could be the reason for your bootloader error trying to use a PSOC 3/5 program on a PSOC 4 device. I have modified the program to work on the PSOC CY8CKIT-049-42XX board. I added the switch to the timer but I have not debugged it that is up to you.