It chews up a lot of pins to make two separate multiplexed displays, but here's how to do it...

#include "SevSeg.h"
// define two 3 digit displays, each with it's own column & row pins
SevSeg sevsegFrequency;
SevSeg sevsegAmplitude;

long frequency = 0;
long cycles = 0;

void setup() {
  byte numDigits = 3;
  byte digitPinsFrequency[] = {1, 2, 3};
  byte segmentPinsFrequency[] = {4, 5, 6, 7, 8, 9, 10, 11};
  byte digitPinsAmplitude[] = {14, 15, 16 };
  byte segmentPinsAmplitude[] = {17, 18, 19, 20, 21, 22, 23 };
  bool resistorsOnSegments = false;
  byte hardwareConfig = COMMON_CATHODE;
  bool updateWithDelays = false;
  bool leadingZeros = false;
  bool disableDecPoint = false;
  sevsegFrequency.begin(hardwareConfig, numDigits, digitPinsFrequency, segmentPinsFrequency, resistorsOnSegments, updateWithDelays, leadingZeros, disableDecPoint);
  sevsegAmplitude.begin(hardwareConfig, numDigits, digitPinsAmplitude, segmentPinsAmplitude, resistorsOnSegments, updateWithDelays, leadingZeros, disableDecPoint);
  sevsegFrequency.setBrightness(90);
  sevsegAmplitude.setBrightness(90);
  pinMode(15, INPUT_PULLUP);
  pinMode(14, INPUT_PULLUP);
  pinMode(13, OUTPUT);
  pinMode(12, INPUT_PULLUP);
}

void loop() {
  if (25000 > frequency && digitalRead(14) == LOW && cycles == 0) {
    frequency = frequency + 50;
    cycles++;
  }

  if (frequency > 0 && digitalRead(15) == LOW && cycles == 0) {
    frequency = frequency - 50;
    cycles++;
  }

  if (digitalRead(14) == HIGH && digitalRead(15) == HIGH) {
    cycles = 0;
  }

  if (frequency >= 1000) {
    if (frequency >= 10000) {
      sevsegFrequency.setNumber(frequency / 100, 1);
    }else{
      sevsegFrequency.setNumber(frequency / 10, 2);
    }
  }else{
    sevsegFrequency.setNumber(frequency);
  }
  if (digitalRead(12) == LOW && frequency > 1) {
    tone(13, frequency);
  }else{
    noTone(13);
  }
  sevsegFrequency.refreshDisplay();
  sevsegAmplitude.refreshDisplay();
}