AVR Freaks

Its nice to hear that you have got the basic communication working like it is supposed to be.

Actually you are sort of lucky because I am also working on a project whereby I am using 2 SAM4S based boards (ATSAM4S-EK2 and ATMSAM4S xplained) and FreeRTOS running on both boards, so I may be able to share information/ideas/code.

If I were you in this situation I would  have a general set_config() function along the lines of

uint32_t atsam4s_set_config(uint8_t uc_config)
{
    return atsam4s_read_register(ATSAM4S_CONFIG_REG, p_config);
}

static uint32_t atsam4s_read_register(uint32_t ul_reg_index, uint8_t *p_reg)
{
	twi_package_t rx = {
		.chip = BOARD_ATSAM4S_ADDR,
		.addr = {ul_reg_index},
		.addr_length = 1,
		.buffer = p_reg_value
	};

	if (ul_reg_index == ATSAM4S_CONF_REG) {
		rx.length = 1;
	} else {
		rx.length = 2;
	}

	return twi_master_read(BOARD_ATSAM4S_TWI_INSTANCE, &rx);
}

static uint32_t atsam4s_write_register(uint32_t ul_reg_index,
		uint8_t *p_reg_value)

{
	twi_package_t tx = {
		.chip = BOARD_ATSAM4S_ADDR,
		.addr = {ul_reg_index},
		.addr_length = 1,
		.buffer = p_reg_value
	};

	if (ul_reg_index == ATSAM4S_CONF_REG) {
		tx.length = 1;
	} else {
		tx.length = 2;
	}

	return twi_master_write(BOARD_ATSAM4S_TWI_INSTANCE, &tx);
}		

Mind you, this code is untested and is meant only to give you the general direction. This is a quick and dirty way of doing what you want.