Unfortunately EI can be very frustrating to deal with. I've been on the verge of throwing it out the window at times, too. It's a good program, it just has issues that really should be addressed.
What do you mean when you say internal use? I send out these statements to my customers who have outstanding balances. You can put the method of payment in the reference box during the payment process if you need that to show on the statement. Are you using a gateway for credit card payments? If so, that's beyond my experience with EI. We do our cc payments separately from EI. I don't know how they look on the customer's account when done through a gateway.
You can also go into your preferences and change the name of the statement so it says "Final Invoice" or some such thing. But be careful if you use the statement for other uses, too. EI will change the name for every one you print until you change it back to "Statement". If you don't use the statement for anything else, then it's not a problem. This would be done from the host computer. I don't think you can do it from the web access.
I saw your post on the 1 cent problem. I've had to manipulate mine that way, too. We sell products online and in person. The online program automatically bills the customer and gives me the order. When I enter it into EI, I've often had to adjust the price to make it match the online one because of the taxes applied. I have found no way to adjust the rounding factor.
I'm using 3.99 on a Mac.
Sorry to not be more help. I just try to answer these because I found it so very frustrating to post something here and nobody answers.