There are special areas within the generated files that allow for code insertion by you. These areas are clearly marked.
Generally I would suggest to avoid making changes in those files. There are two different ways to circumvent this:
Use _StartEx() APIs of the component to announce your own interrupt handlers, might be in main(). Use CY_ISR and CY_ISR_PROTO as documented in System Reference Guide (from Help-menu of Creator)
Latest Creator version introduces "Callback Macros". A file named cyapicallbacks.h is generated with a new project. Here you specify from which API you want to have a callback and you provide a function with a given name to be called back. See Creator Help for "Callback macros)
Oh yes..got it. Thanks a lot Bob.