Check out this thread: http://www.cypress.com/forum/psoc-4-architecture/what-rtos-can-be-used-psoc-4
I'm not sure I understand your questions very well, but:
1. When you load code into the PSoC, it will run. Since FreeRTOS is probably different than other code, it will run differently?
2. Since PSoC creator is an IDE, you can write, build, compile, and program the BLE chip all in the PSoC Creator. FREERTOS is probably just a source code .zip, or contains makefiles. I imagine it would be handled differently, but the C code itself should be easily portable.
3. You can use the PSoC Creator, or the PSoC Programmer software to program the device using a cypress-compatible programmer device. (Takes .hex files as input)
4. The PSoC is a single hex based image chip, and thus you would build and program all libraries and code that you want to be on the chip into the .hex file that you program into the chip the first time. (This isn't a linux OS)
Try checking out the FREERTOS help page and getting started page instead?:http://www.freertos.org/FreeRTOS-quick-start-guide.html
I think all your questions are more FreeRTOS related than PSoC, adding FreeRTOS files to a PSoC Creator project is straight forward, just follow the FreeRTOS getting started tutorials.
1. You will be running a RTOS instead bare metal.
2. No difference, and yes, you will be able to flash the program using Creator.
3. See e.pratt answer (FreeRTOS quick start guide)
4. FreeRTOS specific, non Creator.
Check this project https://cypress.hackster.io/42177/free-rtos-with-psoc-4-ble-82a61e it can help you, there's a PSoC 4BLE + FreeRTOS project attache at the end of the post.
Thank you very much for your help, and you are totally right, I have already started the Getting Started Guide, and some doubts that I had have been cleared. In a moment I will upload in this same forum some of my conclusions and advances.