It can be difficult since as you stated, most insurance carriers have their own format for EOBs. But usually each eob, even though different in format contains the same information, just labeled differently. The key is to look for fields like "patient responsibility" or "allowed amount". Those are usually common on most eobs. Sometimes it requires you to calculate the adjustment, sometimes the adjustment is stated. Some adjustments are called "adjustments", some "provider discounts", or "disallowed amount". Whatever it is called, it means the same thing, the patient doesn't owe it. Most eobs contain at least two different figures that will allow you to double check. For example, if they have a disallowed amount and patient responsibility then once you enter the disallowed amount and the payment, the balance should match the patient responsibility. If they give the allowed amount and the patient responsibility, again once you enter all information the numbers should match up. The key is to go slow in the beginning and make sure you are getting the numbers input right, and then double checking to make sure the balance is truly patient responsibility.
After a bit you will find that you are picking out the numbers quicker and it's not as difficult going from eob to eob.