Refactoring the code

I guess, your goal is to get the total, so I will remove anything you don't need to that goal. Please tell me otherwise in a reply and I will update my answer :)

I will not go into detail how the loop works, because there are very good sites and tutorials for that (best one: MDN). Instead, I will show you step-by-step how I would improve the code.

You can get the total with any of the below code snippets for an undefined number of fields!

const coolObject = {
  "one": {
    "number1": 1,
    "number2": 2
  },
  "two": {
    "number1": 3,
    "number2": 4
  },
  "three": {
    "number1": 5,
    "number2": 6
  }
}

0. (OPTIONAL) You don't have to use strings for field names (safing bytes) and in order to make the code more git-friendly, you should have a dangling comma after every field. Don't forget the semicolon at the end of the variable assignment!

const coolObject = {
  one: {
    number1: 1,
    number2: 2,
  },
  two: {
    number1: 3,
    number2: 4,
  },
  three: {
    number1: 5,
    number2: 6,
  },
};

1. Using a for-loop:

let total = 0;

// iterate over all fields of coolObject
for (numberContainer in coolObject) {
  // iterate over all fields of the fields of coolObject
  for (number in coolObject[numberContainer]) {
    // add the number to the total
    total += coolObject[numberContainer][number];
  }
}

2. Implement error handling:

let total = 0;

// iterate over all fields of coolObject
for (containerField in coolObject) {
  const numberContainer = coolObject[containerField];

  // skip field if it is not an object
  if (
    typeof numberContainer !== 'object' ||
    !coolObject.hasOwnProperty(containerField)
  ) continue;

  // iterate over all fields of the fields of coolObject
  for (numberField in numberContainer) {
    const number = numberContainer[numberField];

    // skip field if it is not a number
    if (
      typeof number !== 'number' ||
      !numberContainer.hasOwnProperty(numberField)
    ) continue;

    // add the number to the total
    total += number;
  }
}

3. Make total const:

const total = (() => {
  let tmp = 0;

  // iterate over all fields of coolObject
  for (containerField in coolObject) {
    const numberContainer = coolObject[containerField];

    // skip field if it is not an object
    if (
      typeof numberContainer !== 'object' ||
      !coolObject.hasOwnProperty(containerField)
    ) continue;

    // iterate over all fields of the fields of coolObject
    for (numberField in numberContainer) {
      const number = numberContainer[numberField];

      // skip field if it is not a number
      if (
        typeof number !== 'number' ||
        !numberContainer.hasOwnProperty(numberField)
      ) continue;

      // add the number to the total
      tmp += number;
    }
  }

  return tmp;
})();

4. (OPTIONAL) We could optimize the whole procedure and make it more functional, if we are able to change the coolObject to use Arrays instead of fields and Objects:

const coolArray = [
  [1,2],
  [3,4],
  [5,6],
];

That would allow us to use convenience methods on the arrays:

const total = coolArray.reduce(
  (acc, arr) => acc + arr.reduce(
    (acc, number) => acc + number,
    0
  ),
  0
);

5. (OPTIONAL) Above form can be enhanced again with error management:

const total = coolArray.reduce(
  (acc, arr) => !Array.isArray(arr)
    ? acc
    : acc + arr.reduce(
      (acc, number) => typeof number !== 'number'
        ? acc
        : acc + number,
      0
    ),
  0
);