You can jump to application using asm code directly in startup files as shown in the app note or you can use C code like this:
typedef void (*func_ptr)();
(*(func_ptr)entry_point)();
Interrupts can be used in both projects, of course, but make sure that all interrupts are disabled before jumping to app. And not only by MSR[EE] but also by all local enable bits in peripherals. I wrote that here just two days ago:
