the device has a boatload of registers that get loaded when the device boots to make it act like the device you captured in PSoC creator. Some configure UDBs, some configure analog blocks, some configure the DSI, and there are others. Those registers are loaded via DMA at bootup. I'd like to know what non-volatile memory that information is stored in. If its the same FLASH where program memory is stored, I'd like to know what the upper limit on the configuration register boot table is. Does that help clarify?
By default the configuration data is located in regular CPU-addressable flash. I do not have a ceiling number of bytes but it is usually a small number of kB. However, you can use the ECC memory instead of flash. In the CYDWR file, System tab, check the Store configuration data in ECC memory box. Then you get to keep all the flash for your application. I've never heard of a design that cannot fit all configuration data in ECC memory.