ATMEL Mega1284P evaluation board avalible

Ok. I think I understand.

In Sd2PinMap.h I need to set these 4 pins as SS, MOSI, MISO, SCK
// PWM (D 10) PB4 5
// MOSI (D 11) PB5 6
// MISO (D 12) PB6 7
// SCK (D 13) PB7 8

Then in any SdFat sketch I run I need to set the PB4 pin as an output.
Then somewhere else this gets called

uint8_t const SD_CHIP_SELECT_PIN = SS_PIN;
Does that need to go in the sketch as well?
Or does this go into Sd2PinMap.h also, with SS_PIN replaced by the physical pin # (18) or by the mapped name (30)?

I have PB4 connected to the shield header so that a user can have 'normal' SPI operations to an external device and not impact the SD card.

Thanks for the additional clarifications. Didn't realize what I had gotten myself into software-wise with my desire to implement increased hardware flexibility.