Unfortunately you've hit the nail right on the head. We've been having the same problem from day one here. I've certainly let the folks back at AC, including Jon aware of it and let them know that we would like it to work better. Hey until recently, the invoices didn't even total, copay and sub-total...No joke. You should write to them and call them and let them know your displeasure with the present situation...It seems that when folks write and call things sometime get changed.
Worse yet, we found a real good bug in the the general totals of your daily reports, this times that should equal the other thing. So like total charges should equal average cost of the encounters times the number of encounters. Of all the things that would go wrong with this program, I never expected it to be something simple like basic math. No need to re-invent the wheel here. PC have been crunching numbers all their life. Although it seems to behaving itself better now after Nancy and I made a big stink about it, we all now have the disclaimer to not trust it. That was added in response to our complaints, post facto...nice, right? So now I'm on the "naughty" list back at AC. I started a thread on "Bad Math" a while back. You should be able to search to it.
But supposedly they are "working on it" and they are going to be designing some sort of a inter-related PM module at some point "soon". But now we're a bit leary here after how the whole thing went down and the recent updates to the EULA. I "Strongly" recommend that all users really re-read the EULA with their eyes wide open and truely understand what it really means if and when one might have a falling out with the vendor. The EULA that is part of the newest versions we are all working with today is not the EULA that we all accepted a year ago or more. I was talking to another doc about this and he too remembers the old EULA, that had actual curse words that as he put it "it seemed like Jon had probably written himself". The first time I read the old one, I split a gut and made the whole office read it. I said, "now there's a company we can go with, these folks are OK. Trashing all the other high and mighty EMR vendors and making them out to be the villians that they really are".
But now our AC EULA is just like all the rest. Seriously, especially you more long term users who may just click on the thing everytime you do an update without giving it a second thought....Because you thought you already knew what was in there... Read it, now. Really carefully read it. It is NOT the old EULA that you first accepted and fell in love with. Take it from us, we know. It was clearly laid out for us one day not too long ago and it was a very strange day here at Village Medical of CNY when it was. Corporate philosopies do tend to change and evolve....

(Nancy here) To distinguish what you are putting on your invoice, use the BILLING NOTES box to the left of the COPAY section. I enter free text there which will show up on the invoice. This does not help with number crunching but does help let everyone know what's going on. I put who the pre-op is for, they still owe a copay, anything.
(Paul) We also use a phrase here, PIFATOS and it is a separate Insurance in our drop-down box. It stands for Pay in Full at Time of Service. That way we can separately track those folks and their totals somewhat. Also below copays we enter cash or ck# 123 or what have you too. I also enter the ck# in our QuickBooks. It helps somewhat.
Paul & Nancy