I am using two shields that but use SPI. one of them uses the 6 pin header and the other uses pins 11,12,and 13. my question is, what is the point in having the 6 pin header if the SPI pins are already located on digital pins?
The 6 pin header does not have a Slave Select signal available on it.
It is intended for connecting an ICSP Programmer.
I don't know why some shields connect to signals there vs getting them from the headers. Maybe it made for easier signal routing on the shield.
So does the 6 pin header have any affect on a shield using the 3 SPI pins above it
No, its the same signals, connected in parallel: SCK, MISO, MOSI, Reset, +5V, Gnd.