First off ditch that library. It's completely pointless and actually makes things harder.

Secondly connect your sensors to the SPI pins, selecting a new CS pin for each sensor.

• Arduino SCK (pin 13) to all the SCK pins.
• Arduino MISO (pin 12) to all the SO pins.
• Individual GPIO pins to individual CS pins (use pin 10 for one of them).

Then just use a simple function to read the data using the SPI library (adapted from the library you link to). For instance with CS on 10 an 9:

#include <SPI.h>

double readCelsius(uint8_t cs) {
    uint16_t v;

    digitalWrite(cs, LOW);
    v = SPI.transfer(0x00);
    v <<= 8;
    v |= SPI.transfer(0x00);
    digitalWrite(cs, HIGH);

    if (v & 0x4) {
        // uh oh, no thermocouple attached!
        return NAN; 
    }

    v >>= 3;

    return v*0.25;
}

void setup() {
    SPI.begin();
    pinMode(10, OUTPUT);
    pinMode(9, OUTPUT);
    digitalWrite(10, HIGH);
    digitalWrite(9, HIGH);
 
    Serial.begin(115200);
}

void loop() {
    Serial.print(readCelcius(10));
    Serial.print(" ");
    Serial.println(readCelcius(9));
    delay(1000);
}

First off ditch that library. It's completely pointless and actually makes things harder.

Secondly connect your sensors to the SPI pins, selecting a new CS pin for each sensor.

• Arduino SCK (pin 13) to all the SCK pins.
• Arduino MISO (pin 12) to all the SO pins.
• Individual GPIO pins to individual CS pins (use pin 10 for one of them).

Then just use a simple function to read the data using the SPI library (adapted from the library you link to). For instance with CS on 10 an 9:

#include <SPI.h>

double readCelsius(uint8_t cs) {
    uint16_t v;

    digitalWrite(cs, LOW);
    v = SPI.transfer(0x00);
    v <<= 8;
    v |= SPI.transfer(0x00);
    digitalWrite(cs, HIGH);

    if (v & 0x4) {
        // uh oh, no thermocouple attached!
        return NAN; 
    }

    v >>= 3;

    return v*0.25;
}

void setup() {
    SPI.begin();
    pinMode(10, OUTPUT);
    pinMode(9, OUTPUT);
    digitalWrite(10, HIGH);
    digitalWrite(9, HIGH);
 
    Serial.begin(115200);
}

void loop() {
    Serial.print(readCelsius(10));
    Serial.print(" ");
    Serial.println(readCelsius(9));
    delay(1000);
}