TTL flash issue and SPI flash advice

hello, I have just purchased a Arduino mega pro and its COM port is not being detected and it is not responding when I try to flash it using a FTDI directly so my guess is the CH308 or whatever it is call is defective (I could scope it later to know for sure). Any how i am able to flash it via SPI with my JTAGICE3 and Atmel studio (after working out the pins on the SPI header which where all wrong) I uploaded blink with some Serial output including the bootloader and I can read the Serial data fine so it is not a short and adding a new bootloader did not fix the Serial flashing. So it must be the ttl chip ?

I have another question too, when flashing with SPI and I have my SPI device still connected (Ra8875 display) is it correct that I must have the CS of the SPI device pulled high with a 4.7k resistor at all times so when i flash it they do not conflict? I hear its the best method to maintain the fastest speeds?

I would just return the mega2560 but I am just getting to the fun part of my latest project and do not want to wait for a replacement

Edit: On second thought my RA8875 display is connected via an 8 channel LLC which has its own enable pin so when if i connect it all up and try to flash it, it may be OK as is currently configured?

If the Mega board has a USB to Serial adapter on it already, I dont see where you would connect a separate FTDI adapter or why you would want to use one.

Devices on the SPI bus do need a pullup on CS, they interfere with the ISP programmer otherwise.

You can burn sketches with the ISP programmer direct from the Arduino IDE.