Peter,
If I may suggest, you might want to nail down with things do and do not show up on the Department report, and which things do or do not show up in the z-out. As Ronald is saying, there are things that don't show up everywhere you might think they should.
As an example, I first tried to capture our shipping charges by using the "Handling" charge during the Finish process. Well, all the money collected showed up on the z-out, but there was no mention of any charge being made for it (so, nothing to balance it with). So we made a series of Items called "shipping-west coast", "shipping east coast", etc., put them in a Category called Shipping and in a Department called "Miscellaneous". That way, any shipping charge shows up on the z-out under both Department and Category, and shows up in any other report I decide to run, too.
Another area that I've found I have to do a little manual input is with deposits and layaways. They don't show up on the z-out as I'd like, but I have a function in Quickbooks where I can add it manually - I just have to have a "trigger" to know that I need to do it (I have the cashier print out an extra receipt that I get with the z-out report). But I've ALWAYS found that if my z-out doesn't balance, it's something I'm missing and not something the software is doing wrong.
I'm not sure Ronald would endorse this, but I keep a copy of the software on a separate computer to run different scenarios like this. I've run all sorts of transactions with various settings this way to figure out how everything works, and it's helped immensely. And it keeps a lot of "voids" out of the live version!