Collecting data from a timer interrupt and storing it into an array
Storing the data into arrays is not an end in itself. The question is:
what do you want to do with these arrays? The way to proceed depends on
that purpose.
If you want the data acquisition (analogRead()) and the processing
(computation and printing) to proceed in parallel, then you will need
the arrays for buffering the data between those two processes. As
mentioned by Michel Keijzers in his answer, you will have to research
the concept of ring buffer.
There is a ring buffer implementation in the Arduino core you can use as
inspiration: when reading data from the Serial port, the incoming bytes
are received by an ISR and stored in a ring buffer. The
Serial.read() method can then be used to retrieve these bytes
and process them outside the interrupt context.
Another option is to alternate between an acquisition phase and a
processing phase. This can be an interesting approach if the acquisition
rate is too fast for the processing to be performed in real time. In
this case, you do not need a ring buffer. Instead, you have the ISR fill
the arrays and, when they are full, the main program can take on and
start the processing. For coordinating these jobs, you just need a
boolean to keep track of whether you are performing the acquisition
phase or the processing phase. Note that, since accessing a boolean is
an atomic operation, you do not need to disable interrupts for this.
Here is an example implementation of this strategy. The variable
sampling_done is used to coordinate the two processes:
const size_t sample_count = 256;

volatile int gauge0[sample_count];
volatile int gauge1[sample_count];
volatile bool sampling_done = false;

ISR(TIMER1_COMPA_vect) {
    if (sampling_done) return;  // nothing to do

    static size_t sample_idx = 0;
    gauge0[sample_idx] = analogRead(A0);
    gauge1[sample_idx] = analogRead(A1);
    if (++sample_idx &gt;= sample_count) {
        sample_idx = 0;  // prepare for next round
        sampling_done = true;
    }
}

void process_samples(int Gauge0, int Gauge1) {
    // Whatever needs to be done with the samples:
    // computation, printing...
}

void loop() {
    if (sampling_done) {
        for (size_t i = 0; i &lt; sample_count; i++) {
            process_samples(gauge0[i], gauge1[i]);
        }
        sampling_done = false;  // start next sampling round
    }
}

Now some random remarks:

There is no need to sei() in setup(): interrupts have already been
enabled by the Arduino core initialization.

Do not reset TCNT1 within the ISR: this is handled automatically by
the CTC mode. If you do this in software, you risk missing timer
ticks.

Do not store the readings in float variables: they take twice the
memory of an int and all operations on floats are incredibly slow
compared to the equivalent operations on ints.

The scale factor for converting the readings to percent scale is
100.0/1024: the maximum possible analog reading (1023) is one ADC
step below the reference voltage: see the datasheet.

You should remove unused variables as soon as they become unused
(count, num, AVG). Once you do that you should notice you do not
need floats at all.